Plastidic phosphoglucomutase genes

ABSTRACT

An isolated nucleic acid fragment encoding a plastidic phosphoglucomutase protein is disclosed. Also disclosed is the construction of a chimeric gene encoding all or a substantial portion of the plastidic phosphoglucomutase, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the plastidic phosphoglucomutase in a transformed host cell.

This application is a Continuation-in-Part and claims the benefit ofU.S. patent application Ser. No. 09/906,209, filed Jul. 16, 2001, nowpending, and U.S. Provisional Application No. 60/218,712, filed Jul. 17,2000, now expired, the entire contents of both are herein incorporatedby reference.

FIELD OF THE INVENTION

This invention is in the field of plant molecular biology. Morespecifically, this invention pertains to isolated nucleic acid fragmentsencoding plastidic phosphoglucomutase proteins in plants and seeds andthe use of such fragments to modulate expression of a gene encodingplastidic phosphoglucomutase activity.

BACKGROUND OF THE INVENTION

Starch synthesis occurs in the chloroplast while soluble carbohydrate(i.e., sucrose) synthesis occurs in the cytosol. These biosyntheticpathways are competing processes because excess triose phosphate can beused for either starch synthesis in the chloroplast or sucrose synthesisin the cytosol. These pathways have many common steps, however, theenzymes that catalyze similar steps are unique to each compartment.These enzymes are isozymes; different forms of the enzymes that catalyzethe same reaction. For example, the plastidic and cytosolic forms ofphosphoglucomutase both catalyze the conversion of glucose-6-phosphateto glucose 1-phosphate in different subcellular locations.

At maturity, about 40% of soybean seed dry weight is protein and 20%extractable oil. These constitute the economically valuable products ofthe soybean crop. Of the remaining 40% of seed weight, about 10% issoluble carbohydrate. The soluble carbohydrate portion contributeslittle to the economic value of soybean seeds and the main component ofthe soluble carbohydrate fraction, raffinosaccharides, are deleteriousboth to processing and to the food value of soybean meal in monogastricanimals (Coon et al., (1988) Proceedings Soybean UtilizationAlternatives, Univ. of Minnesota, pp. 203-211).

It may be possible to modulate the size of the starch and solublecarbohydrate pools in plant cells by altering the catalytic activity ofspecific enzymes in the starch and soluble carbohydrate biosyntheticpathways, such as phosphoglucomutase or one or both of the large andsmall subunits of ADP-glucose pyrophosphorylase (Taiz L., et al. PlantPhysiology; The Benjamin/Cummings Publishing Company: New York, 1991).For example, during soybean seed maturation a large portion of theglucose which is converted to soluble carbohydrates (sucrose, raffinoseand stachyose) during soybean seed maturation comes from the break downof a starch pool which was produced slowly during the primary growthphase. Elimination of this transient starch pool may be a strategy fordiverting carbon away from the soluble carbohydrate components of drysoybean seeds (sucrose, raffinose and stachyose) and into the moreeconomically desirable components such as oil and protein. This strategymay also be applicable to other plants such as corn, rice and wheat.Elimination of ADP-glucose pyrophosphorylase expression in developingmaize embryos may decrease the production of transient starch in thattissue and lead to a concomitant increase in the oil content of theembryo [Singletary, G et al. (2001) U.S. Pat. No. 6,232,529].

There is a great deal of interest in identifying the genes that encodeproteins involved in starch and soluble carbohydrate biosynthesis inplants. The genes that code for these enzymes may be used to study theinteractions among individuals of the pathways and develop methods toalter starch and soluble carbohydrate biosynthesis. Accordingly, theavailability of nucleic acid sequences encoding all or a substantialportion of a plastidic or cytosolic phosphoglucomutase (PGM) enzymewould facilitate studies to better understand starch and solublecarbohydrate biosynthesis in plants and provide genetic tools to enhanceor otherwise alter starch and soluble carbohydrate biosynthesis.

Previous reports on a plastidic PGM mutant (pgm-1) from the oilseedplant Arabidopsis (Caspar et al. (1985) Plant Physiol. 79:11-17;Periappuram et al., (2000) Plant Physiol. 122:1193-1199) indicated thatpgm-1 mutant plants showed a decrease in seed lipid content and anincrease in leaf soluble carbohydrates. High levels of solublecarbohydrates were also observed in starchless Nicotiana sylvestrisplants deficient in the plastidic PGM activity (Huber and Hanson, (1992)Plant Physiol. 99:1449-1454). Yet another effect of reduced starchcontent on carbon partitioning was observed in pea (Pisum sativum).Seeds from wild type pea typically contain 60% of the seed dry weight asstarch. The rug3 locus of Pisum sativum encodes the pea plastidicphosphoglucomutase. Pea seeds, of the rug3rug3 genotype, substantiallylacking plastidic phosphoglucomutase activity, have a wrinkledphenotype, higher levels of sucrose and an increased lipid content atmaturity (EP 1001029A1; Casey et al., (1998) J. Plant Physiol. 152:636-640).

SUMMARY OF THE INVENTION

In a first embodiment, the present invention concerns an isolatedpolynucleotide comprising: (a) a first nucleotide sequence encoding afirst polypeptide comprising at least 560 amino acids, wherein the aminoacid sequence of the first polypeptide and the amino acid sequence ofSEQ ID NO:8 have at least 95%, 96%, 97%, 98%, 99% or 100% sequenceidentity, based on the Clustal V method of alignment, (b) a secondnucleotide sequence encoding a second polypeptide comprising at least560 amino acids, wherein the amino acid sequence of the secondpolypeptide and the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, orSEQ ID NO:10 have at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100%sequence identity, based on the Clustal V method of alignment, or (c)the complement of the first or second nucleotide sequence, wherein thecomplement and the first or second nucleotide sequence contain the samenumber of nucleotides and are 100% complementary. The first polypeptidepreferably comprises the amino acid sequence of SEQ ID NO:8, and thesecond polypeptide preferably comprises the amino acid sequence of SEQID NO:2, SEQ ID NO:4, or SEQ ID NO:10. The first nucleotide sequencepreferably comprises the nucleotide sequence of SEQ ID NO:7, the secondnucleotide sequence preferably comprises the nucleotide sequence of SEQID NO:1, SEQ ID NO:3, or SEQ ID NO:9. The first and second polypeptidespreferably have phosphoglucomutase activity.

In a second embodiment, the present invention relates to a recombinantDNA construct comprising any of the isolated polynucleotides of thepresent invention operably linked to at least one regulatory sequence.

In a third embodiment, the present invention relates to a vectorcomprising any of the isolated polynucleotides of the present invention.

In a fourth embodiment, the present invention relates to an isolatedpolynucleotide fragment comprising a nucleotide sequence comprised byany of the polynucleotides of the present invention, wherein thenucleotide sequence contains at least 30, 40, 60, 100, 200, 300, 400,500 or 541 nucleotides.

In a fifth embodiment, the present invention relates to a method fortransforming a cell comprising transforming a cell with any of theisolated polynucleotides of the present invention, and the celltransformed by this method. Advantageously, the cell is eukaryotic,e.g., a yeast or plant cell, or prokaryotic, e.g., a bacterium.

In a sixth embodiment, the invention concerns a method for transforminga cell, comprising transforming a cell with a polynucleotide of thepresent invention.

In a seventh embodiment, the present invention relates to a method forproducing a transgenic plant comprising transforming a plant cell withany of the isolated polynucleotides of the present invention andregenerating a transgenic plant from the transformed plant cell.

In an eighth embodiment, the invention concerns a cell, plant, or seedcomprising a recombinant DNA construct of the present invention.

In a ninth embodiment, the present invention concerns an isolatedpolypeptide comprising: (a) a first amino acid sequence comprising atleast 560 amino acids, wherein the first amino acid sequence and theamino acid sequence of SEQ ID NO:8 have at least 95%, 96%, 97%, 98%, 99%or 100% sequence identity, based on the Clustal V method of alignment,and (b) a second amino acid sequence comprising at least 560 aminoacids, wherein the second amino acid sequence and the amino acidsequence of SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:10 have at least 85%,90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity, based on theClustal V method of alignment. The first amino acid sequence preferablycomprises the amino acid sequence of SEQ ID NO:8, and the second aminoacid sequence preferably comprises the amino acid sequence SEQ ID NO:2,SEQ ID NO:4, or SEQ ID NO:10. The polypeptide preferably hasphosphoglucomutase activity.

In a tenth embodiment, the present invention relates to a virus,preferably a baculovirus, comprising any of the isolated polynucleotidesof the present invention or any of the recombinant DNA constructs of thepresent invention.

In an eleventh embodiment, the invention relates to a method ofselecting an isolated polynucleotide that alters, i.e., increases ordecreases, the level of expression of a phosphoglucomutase gene, proteinor enzyme activity in a host cell, preferably a plant cell, the methodcomprising the steps of: (a) constructing an isolated polynucleotide ofthe present invention or an isolated recombinant DNA construct of thepresent invention; (b) introducing the isolated polynucleotide or theisolated recombinant DNA construct into a host cell; (c) measuring thelevel of the phosphoglucomutase RNA, protein or enzyme activity in thehost cell containing the isolated polynucleotide or recombinant DNAconstruct; (d) comparing the level of the phosphoglucomutase RNA,protein or enzyme activity in the host cell containing the isolatedpolynucleotide or recombinant DNA construct with the level of thephosphoglucomutase RNA, protein or enzyme activity in a host cell thatdoes not contain the isolated polynucleotide or recombinant DNAconstruct, and selecting the isolated polynucleotide or recombinant DNAconstruct that alters, i.e., increases or decreases, the level ofexpression of the phosphoglucomutase gene, protein or enzyme activity inthe plant cell.

In a twelfth embodiment, the invention concerns a method of obtaining anucleic acid fragment encoding a substantial portion of aphosphoglucomutase protein, preferably a plant phosphoglucomutaseprotein, comprising the steps of: synthesizing an oligonucleotide primercomprising a nucleotide sequence of at least 30 contiguous nucleotides,preferably at least 40 contiguous nucleotides, more preferably at least60 contiguous nucleotides derived from a nucleotide sequence selectedfrom the group consisting of SEQ ID NOs:1, 3, 5, 7, and 9, and thecomplement of such nucleotide sequences; and amplifying a nucleic acidfragment (preferably a cDNA inserted in a cloning vector) using theoligonucleotide primer. The amplified nucleic acid fragment preferablywill encode a substantial portion of a phosphoglucomutase protein aminoacid sequence.

In a thirteenth embodiment, the invention relates to a method ofobtaining a nucleic acid fragment encoding all or a substantial portionof the amino acid sequence encoding a phosphoglucomutase proteincomprising the steps of: probing a cDNA or genomic library with anisolated polynucleotide of the present invention; identifying a DNAclone that hybridizes with an isolated polynucleotide of the presentinvention; isolating the identified DNA clone; and sequencing the cDNAor genomic fragment that comprises the isolated DNA clone.

In a fourteenth embodiment, the invention concerns a method for positiveselection of a transformed cell comprising: (a) transforming a host cellwith the recombinant DNA construct of the present invention or anexpression cassette of the present invention; and (b) growing thetransformed host cell, preferably a plant cell, such as a monocot or adicot, under conditions which allow expression of the phosphoglucomutasepolynucleotide in an amount sufficient to complement a null mutant toprovide a positive selection means.

In a fifteenth embodiment, this invention concerns a method forsuppressing the level of expression of a gene encoding a plastidicpolypeptide having phosphoglucomutase activity in a transgenic plant,wherein the method comprises:

-   -   (a) transforming a plant cell with a fragment of the isolated        polynucleotide of the invention;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant wherein the level of expression        of a gene encoding a plastidic polypeptide having        phosphoglucomutase activity has been suppressed.

Preferably, the gene encodes a plastidic polypeptide havingphosphoglucomutase activity, and the plant is a soybean plant.

In a sixteenth embodiment, the invention concerns a method for producingtransgenic seed, the method comprising:

-   -   (a) transforming a plant cell with the recombinant DNA construct        of    -   (i) all or part of the nucleotide sequence set forth in SEQ ID        NO:7 or SEQ ID NO:15; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous phosphoglucomutase activity in a        transgenic plant;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        having an increase in the combined oil and protein content of at        least 1.6% and a decrease in the sucrose content of at least 25%        as compared to seed obtained from a non-transgenic plant.

Preferably, the seed is a soybean seed.

In a seventeenth embodiment, the invention concerns a method method forproducing transgenic seed, the method comprising:

-   -   (a) transforming a plant cell with a recombinant DNA construct        comprising    -   (i) all or part of the nucleotide sequence set forth in SEQ ID        NO:7 or SEQ ID NO:15; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous phosphoglucomutase activity in a        transgenic plant;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        having a sucrose to raffinose family oligosaccharide ratio of        1.0 or less as compared to seed obtained from a non-transgenic        plant.

Preferably, the transgenic seed differs from an untransformed seed byhaving an increase in the combined oil and protein content of at least1.6%, 1.8% or 2.0%. Preferably, the seed is a soybean seed.

In an eighteenth embodiment, the invention concerns a method forproducing defatted meal from transgenic seed, comprising:

-   -   (a) transforming a plant cell with a recombinant DNA construct        comprising (i) all or part of the nucleotide sequence set forth        in SEQ ID NO:7 or SEQ ID NO:15; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous phosphoglucomutase activity in a        transgenic plant;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        wherein said seed is processed into defatted meal having an        increase in the combined oil and protein content of at least 5%        and a decrease in the sucrose content of at least 25% as        compared to defatted meal obtained from seed of a non-transgenic        plant.

Preferably, the defatted meal of the transgenic seed differs from thedefatted meal of an untransformed seed by having a sucrose to raffinosefamily oligosaccharide ratio of 1.0 or less. Preferably, the seed is asoybean seed.

In a nineteenth embodiment, the invention concerns a transgenic seedthat differs from an non-transgenic seed by having an increase in thecombined oil and protein content of at least 1.6%, 1.8% or 2.0%, and adecrease in the sucrose content of at least 25%. Preferably, the seed isa soybean seed.

In a twentieth embodiment, the invention concerns a transgenic seed thatdiffers from non-transgenic seed by having a sucrose to raffinose familyoligosaccharide ratio of 1.0 or less. Preferably, the transgenic seeddiffers from an untransformed seed by having an increase in the combinedoil and protein content of at least 1.6%, 1.8% or 2.0%. Preferably, theseed is a soybean seed.

In a twenty-first embodiment, the invention concerns a transgenic seedcomprising a recombinant construct comprising (i) all or part of thenucleotide sequence set forth in SEQ ID NO:7 or SEQ ID NO:15; or

-   -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous phosphoglucomutase activity in a        transgenic plant;    -   further wherein said transgenic seed is processed to make        defatted meal having an increase in the combined oil and protein        content of at least 5% and a decrease in the sucrose content of        at least 25% when compared to defatted meal obtained from a        non-transgenic seed.

Preferably, the defatted meal of the transgenic seed differs from thedefatted meal of an untransformed seed by having a sucrose to raffinosefamily oligosaccharide ratio of 1.0 or less. Preferably, the seed is asoybean seed.

In a twenty-second embodiment, the invention concerns a recombinant DNAconstruct comprising: (a) all or part of the nucleotide sequence setforth in SEQ ID NO:7 or SEQ ID NO:15; or (b) the complement of (a);wherein (a) or (b) is useful in co-suppression or antisense suppressionof endogenous phosphoglucomutase activity in a transgenic plant.

BRIEF DESCRIPTION OF THE FIGURES AND SEQUENCE LISTING

The invention can be more fully understood from the following detaileddescription and the accompanying Drawing and Sequence Listing which forma part of this application.

FIGS. 1A-1D show an alignment of the amino acid sequences of plastidicphosphoglucomutase encoded by the nucleotide sequences derived from thefollowing: cattail clone etr1c.pk005.f8 (SEQ ID NO:2); corn contig (SEQID NO:4) composed of p0075.cslaf22f (EST), p0075.cslaf22rb (EST), andp0128.cpicz81r (EST); soybean contig (SEQ ID NO:8) composed of clonesdp3c.pk003.e22 and PCR fragments; rice clone rdi1c.pk001.a22 (SEQ IDNO:10); plastidic phosphoglucomutase from Brassica napus (NCBI GeneralIdentifier No. 6272125; SEQ ID NO:11); plastidic phosphoglucomutase fromPisum sativum (NCBI General Identifier No. 6272283; SEQ ID NO:12); andplastidic phosphoglucomutase from Pisum sativum described in EuropeanPatent Application EP 1001029-A (NCBI General Identifier No. 10190529;SEQ ID NO:13). For the consensus alignment, amino acids which areconserved among all sequences at a given position, and which arecontained in at least two sequences, are indicated with an asterisk (*).Dashes are used by the program to maximize alignment of the sequences.Amino acid positions for a given SEQ ID NO are given to the left of thecorresponding line of sequence. Amino acid positions for the consensusalignment are given below each section of sequence.

FIG. 2 shows the starch accumulation expressed as mg/g fresh weight(top) and mg/seed (bottom) in plastidic PGM-silenced seeds (ko) ascompared to wild-type seeds (wt).

FIG. 3 shows the soluble carbohydrate concentrations of growth chamber(GC) or field grown (field) T2 seeds from plastidic PGM-silenced events(KO) as compared to their null segregants (WT).

FIG. 4 shows soluble carbohydrate concentrations of T3 seeds fromplastidic PGM-silenced events as compared to wild-type. PGM-silencedseeds with a 92B91 genetic background were compared to a 92B91 nullevent, while PGM-silenced seeds with a Jack background were compared toa Jack null event.

FIG. 5 shows the soluble carbohydrate profile of defatted soybean mealfrom T2 seeds.

Table 1 lists the polypeptides that are described herein, thedesignation of the cDNA clones that comprise the nucleic acid fragmentsencoding polypeptides representing all or a substantial portion of thesepolypeptides, and the corresponding identifier (SEQ ID NO:) as used inthe attached Sequence Listing. Table 1 also identifies the cDNA clonesas individual ESTs (“EST”), the sequences of the entire cDNA insertscomprising the indicated cDNA clones (“FIS”), contigs assembled from twoor more ESTs (“Contig”), contigs assembled from an FIS and one or moreESTs (“Contig*”), or sequences encoding the entire or functional proteinderived from an FIS, a contig, an EST and PCR, or an FIS and PCR(“CGS”). Nucleotide SEQ ID NOs:1, 3, 5, and 7 correspond to nucleotideSEQ ID NOs:1, 3, 5, and 7, respectively, presented in U.S. ProvisionalApplication No. 60/218,712, filed Jul. 17, 2000. Amino acid SEQ IDNOs:2, 4, 6, and 8 correspond to amino acid SEQ ID NOs:2, 4, 6, and 8,respectively, presented in U.S. Provisional Application No. 60/218,712,filed Jul. 17, 2000. The sequence descriptions and Sequence Listingattached hereto comply with the rules governing nucleotide and/or aminoacid sequence disclosures in patent applications as set forth in 37C.F.R. §1.821-1.825. TABLE 1 Plastidic Phosphoglucomutase Proteins SEQID NO: Protein Amino (Plant Source) Clone Designation Status NucleotideAcid Plastidic etr1c.pk005.f8 (FIS) CGS 1 2 Phospho- glucomutase(Cattail) Plastidic Contig Composed of: CGS 3 4 Phospho- p0075.cslaf22f(EST); glucomutase p0075.cslaf22rb (Corn) (EST); p0128.cpicz81r (EST)Plastidic rth1c.pk009.k14.f EST 5 6 Phospho- (EST) glucomutase (Rice)Plastidic Contig Composed of: CGS 7 8 Phospho- sdp3c.pk003.e22glucomutase (EST); PCR (Soybean) Fragments Plastidic rdi1c.pk001.a22(FIS) CGS 9 10 Phospho- glucomutase (Rice)

SEQ ID NO:10 corresponds to a direct translation of the nucleotidesequence for the full insert of rice clone rdi1c.pk001.a22. The aminoacid sequence in SEQ ID NO:10 includes a 46 amino acid open-readingframe directly in front of, and in frame with, the methionine startcodon.

SEQ ID NO:11 corresponds to plastidic phosphoglucomutase from Brassicanapus (NCBI General Identifier No. 6272125).

SEQ ID NO:12 corresponds to plastidic phosphoglucomutase from Pisumsativum (NCBI General Identifier No. 6272283).

SEQ ID NO:13 corresponds to and plastidic phosphoglucomutase from Pisumsativum described in European Patent Application EP 1001029-A (NCBIGeneral Identifier No. 10190529).

SEQ ID NO:14 corresponds to a 574 nucleotide NotI fragment from plasmidpTC103; this fragment contains a 541 nucleotide region of soybeanplastidic phosphoglucomutase, a 19 nucleotide artificial sequence at the5′ end and a 14 nucleotide artificial sequence at the 3′ end.

SEQ ID NO:15 corresponds to the 541 nucleotide region of soybeanplastidic phosphoglucomutase contained in SEQ ID NO:14.

SEQ ID NO:16 corresponds to the full-insert sequence (FIS) of corn clonep0075.cslaf22rb.

SEQ ID NO:17 corresponds to the nucleotide sequence of plasmid pKS133.

SEQ ID NO:18 corresponds to a synthetic DNA linker.

SEQ ID NO:19 corresponds to synthetic complementary region of pKS106 andpKS124.

SEQ ID NO:20 corresponds to a synthetic complementary region of pKS133.

SEQ ID NO:21 corresponds to a synthetic PCR primer.

SEQ ID NO:22 corresponds to a synthetic PCR primer.

SEQ ID NO:23 corresponds to a nucleotide sequence of a contig made fromthe full-insert sequences of the cDNA inserts of soybean clonesses4d.pk0018.d10 and sdp2c.pk008.m2. The first 107 nucleotides of thecontig were obtained from the sequence of clone ses4d.pk0018.d10.

SEQ ID NO:24 corresponds to the amino acid sequence of a large subunitpolypeptide of soybean ADP-glucose pyrophosphorylase, and is encoded bynucleotides 42-1637 of SEQ ID NO:23.

SEQ ID NO:25 corresponds to the amino acid sequence of the large subunitof ADP-glucose pyrophosphorylase from chickpea, Cicer arietinum (NCBIGeneral Identifier No. 13487785).

SEQ ID NO:26 corresponds to the amino acid sequence of SEQ ID NO:248406from U.S. patent application US2004031072.

SEQ ID NO:27 corresponds to a nucleotide sequence obtained from thefull-length sequence of the cDNA insert of soybean clonessm.pk0072.e7:fis.

SEQ ID NO:28 corresponds to the amino acid sequence of a first smallsubunit polypeptide, SS1, of the soybean ADP-glucose pyrophosphorylase,and is encoded by nucleotides 80-1627 of SEQ ID NO:27.

SEQ ID NO:29 corresponds to a nucleotide sequence of a contig made fromthe EST sequence of soybean clone ssI.pk0021.h3 and the full-insertsequence of soybean clone sgs4c.pk005.b10. The first 58 nucleotides ofthe contig were obtained from the sequence of clone ssI.pk0021.h3.

SEQ ID NO:30 corresponds to the amino acid sequence of a second smallsubunit polypeptide, SS2, of the soybean ADP-glucose pyrophosphorylase,and is encoded by nucleotides 47-1594 of SEQ ID NO:29.

SEQ ID NO:31 corresponds to the amino acid sequence of the smallsubunit, PvAGPS1, of ADP-glucose pyrophosphorylase from Phaseolusvulgaris (NCBI General Identifier No. 29421116).

SEQ ID NO:32 corresponds to the amino acid sequence of SEQ ID NO:251944from U.S. patent application US2004031072.

The Sequence Listing contains the one letter code for nucleotidesequence characters and the three letter codes for amino acids asdefined in conformity with the IUPAC-IUBMB standards described inNucleic Acids Res. 13:3021-3030 (1985) and in the Biochemical J. 219(No. 2):345-373 (1984) which are herein incorporated by reference. Thesymbols and format used for nucleotide and amino acid sequence datacomply with the rules set forth in 37 C.F.R. §1.822.

DETAILED DESCRIPTION OF THE INVENTION

All patents, patent applications, and publications cited throughout theapplication are hereby incorporated by reference in their entirety.

In the context of this disclosure, a number of terms shall be utilized.

The term “raffinose family oligosaccharides” (RFOs) indicates a group ofD-galactose containing oligosaccharides that are synthesized by a set ofgalactosyltransferases. Raffinose family oligosaccharides arecharacterized by having the general formula:O-β-D-galactopyranosyl-(1→6)_(n)-α-D-glucopyranosyl-(1→2)-β-D-fructofuranoside,where oligosaccharides with n=1 through n=4 are known respectively asraffinose, stachyose, verbascose, and ajugose. Examples of raffinosefamily oligosaccharides include, but are not limited to, raffinose,stachyose, verbascose and ajugose.

The term “plant” includes reference to whole plants, plant parts ororgans (e.g., leaves, stems, roots, etc.), plant cells, seeds andprogeny of same. Plant cell, as used herein includes, withoutlimitation, cells obtained from or found in the following: seeds,suspension cultures, embryos, meristematic regions, callus tissue,leaves, roots, shoots, gametophytes, sporophytes, pollen andmicrospores. Plant cells can also be understood to include modifiedcells, such as protoplasts, obtained from the aforementioned tissues.The class of plants which can be used in the methods of the invention isgenerally as broad as the class of higher plants amenable totransformation techniques, including both monocotyledonous anddicotyledonous plants.

Examples of monocots include, but are not limited to, corn, wheat, rice,sorghum, millet, barley, palm, lily, Alstroemeria, rye, and oat.

Examples of dicots include, but are not limited to, soybean, rape,sunflower, canola, grape, guayule, columbine, cotton, tobacco, peas,beans, flax, safflower, and alfalfa.

Plant tissue includes differentiated and undifferentiated tissues orplants, including but not limited to, roots, stems, shoots, leaves,pollen, seeds, tumor tissue, and various forms of cells and culture suchas single cells, protoplasm, embryos, and callus tissue. The planttissue may in plant or in organ, tissue or cell culture.

The term “plant organ” refers to plant tissue or group of tissues thatconstitute a morphologically and functionally distinct part of a plant.The term “genome” refers to the following: 1. The entire complement ofgenetic material (genes and non-coding sequences) is present in eachcell of an organism, or virus or organelle. 2. A complete set ofchromosomes inherited as a (haploid) unit from one parent. The term“stably integrated” refers to the transfer of a nucleic acid fragmentinto the genome of a host organism or cell resulting in geneticallystable inheritance.

The terms “polynucleotide”, “polynucleotide sequence”, “nucleic acid”,nucleic acid sequence”, and “nucleic acid fragment” are usedinterchangeably herein. These terms encompass nucleotide sequences andthe like. A polynucleotide may be a polymer of RNA or DNA that issingle- or double-stranded, that optionally contains synthetic,non-natural or altered nucleotide bases. A polynucleotide in the form ofa polymer of DNA may be comprised of one or more segments of cDNA,genomic DNA, synthetic DNA, or mixtures thereof.

The term “isolated” refers to materials, such as “isolated nucleic acidfragments” and/or “isolated polypeptides”, which are substantially freeor otherwise removed from components that normally accompany or interactwith the materials in a naturally occurring environment. Isolatedpolynucleotides may be purified from a host cell in which they naturallyoccur. Conventional nucleic acid purification methods known to skilledartisans may be used to obtain isolated polynucleotides. The term alsoembraces recombinant polynucleotides and chemically synthesizedpolynucleotides.

The term “isolated nucleic acid fragment” is used interchangeably with“isolated polynucleotide” and is a polymer of RNA or DNA that is single-or double-stranded, optionally containing synthetic, non-natural oraltered nucleotide bases. An isolated nucleic acid fragment in the formof a polymer of DNA may be comprised of one or more segments of cDNA,genomic DNA or synthetic DNA. Nucleotides (usually found in their5′-monophosphate form) are referred to by their single letterdesignation as follows: “A” for adenylate or deoxyadenylate (for RNA orDNA, respectively), “C” for cytidylate or deoxycytidylate, “G” forguanylate or deoxyguanylate, “U” for uridylate, “T” fordeoxythymidylate, “R” for purines (A or G), “Y” for pyrimidines (C orT), “K” for G or T, “H” for A or C or T, “I” for inosine, and “N” forany nucleotide.

The terms “subfragment that is functionally equivalent” and“functionally equivalent subfragment” are used interchangeably herein.These terms refer to a portion or subsequence of an isolated nucleicacid fragment in which the ability to alter gene expression or produce acertain phenotype is retained whether or not the fragment or subfragmentencodes an active enzyme. For example, the fragment or subfragment canbe used in the design of recombinant DNA constructs to produce thedesired phenotype in a transformed plant. Recombinant DNA constructs canbe designed for use in co-suppression or antisense by linking a nucleicacid fragment or subfragment thereof, whether or not it encodes anactive enzyme, in the appropriate orientation relative to a plantpromoter sequence.

“Cosuppression” refers to the production of sense RNA transcriptscapable of suppressing the expression of identical or substantiallysimilar native genes (U.S. Pat. No. 5,231,020). Cosuppression technologyconstitutes the subject matter of U.S. Pat. No. 5,231,020, which issuedto Jorgensen et al. on Jul. 27, 1999. The phenomenon observed by Napoliet al. in petunia was referred to as “cosuppression” since expression ofboth the endogenous gene and the introduced transgene were suppressed(for reviews see Vaucheret et al., Plant J. 16:651-659 (1998); and Gura,Nature 404:804-808 (2000)).

Co-suppression constructs in plants previously have been designed byfocusing on overexpression of a nucleic acid sequence having homology toan endogenous mRNA, in the sense orientation, which results in thereduction of all RNA having homology to the overexpressed sequence (seeVaucheret et al. (1998) Plant J 16:651-659; and Gura (2000) Nature404:804-808). The overall efficiency of this phenomenon is low, and theextent of the RNA reduction is widely variable. Recent work hasdescribed the use of “hairpin” structures that incorporate all, or part,of an mRNA encoding sequence in a complementary orientation that resultsin a potential “stem-loop” structure for the expressed RNA (PCTPublication WO 99/53050 published on Oct. 21, 1999). This increases thefrequency of cosuppression in the recovered transgenic plants. Anothervariation describes the use of plant viral sequences to direct thesuppression, or “silencing”, of proximal mRNA encoding sequences (PCTPublication WO 98/36083 published on Aug. 20, 1998). Both of theseco-suppressing phenomena have not been elucidated mechanistically,although recent genetic evidence has begun to unravel this complexsituation (Elmayan et al. (1998) Plant Cell 10:1747-1757).

In addition to cosuppression, antisense technology has also been used toblock the function of specific genes in cells. Antisense RNA iscomplementary to the normally expressed RNA, and presumably inhibitsgene expression by interacting with the normal RNA strand. Themechanisms by which the expression of a specific gene are inhibited byeither antisense or sense RNA are on their way to being understood.However, the frequencies of obtaining the desired phenotype in atransgenic plant may vary with the design of the construct, the gene,the strength and specificity of its promoter, the method oftransformation and the complexity of transgene insertion events(Baulcombe, Curr. Biol. 12(3):R82-84 (2002); Tang et al., Genes Dev.17(1):49-63 (2003); Yu et al., Plant Cell. Rep. 22(3):167-174 (2003)).Cosuppression and antisense inhibition are also referred to as “genesilencing”, “post-transcriptional gene silencing” (PTGS), RNAinterference or RNAi. See for example U.S. Pat. No. 6,506,559.

MicroRNAs (miRNA) are small regulatory RNSs that control geneexpression. miRNAs bind to regions of target RNAs and inhibit theirtranslation and, thus, interfere with production of the polypeptideencoded by the target RNA. miRNAs can be designed to be complementary toany region of the target sequence RNA including the 3′ untranslatedregion, coding region, etc. miRNAs are processed from highly structuredRNA precursors that are processed by the action of a ribonuclease IIItermed DICER. While the exact mechanism of action of miRNAs is unknown,it appears that they function to regulate expression of the target gene.See, e.g., U.S. patent Publication No. 2004/0268441 AI which waspublished on Dec. 30, 2004.

The term “expression”, as used herein, refers to the production of afunctional end-product, be it mRNA or translation of mRNA into apolypeptide. “Antisense inhibition” refers to the production ofantisense RNA transcripts capable of suppressing the expression of thetarget protein. “Co-suppression” refers to the production of sense RNAtranscripts capable of suppressing the expression of identical orsubstantially similar foreign or endogenous genes (U.S. Pat. No.5,231,020).

“Overexpression” refers to the production of a functional end-product intransgenic organisms that exceeds levels of production when compared toexpression of that functional end-product in a normal, wild type ornon-transformed organism.

“Stable transformation” refers to the transfer of a nucleic acidfragment into a genome of a host organism, including both nuclear andorganellar genomes, resulting in genetically stable inheritance. Incontrast, “transient transformation” refers to the transfer of a nucleicacid fragment into the nucleus, or DNA-containing organelle, of a hostorganism resulting in gene expression without integration or stableinheritance. Host organisms containing the transformed nucleic acidfragments are referred to as “transgenic” organisms. The preferredmethod of cell transformation of rice, corn and other monocots is usingparticle-accelerated or “gene gun” transformation technology (Klein etal. (1987) Nature (London) 327:70-73; U.S. Pat. No. 4,945,050), or anAgrobacterium-mediated method (Ishida Y. et al. (1996) Nature Biotech.14:745-750). The term “transformation” as used herein refers to bothstable transformation and transient transformation.

“Antisense inhibition” refers to the production of antisense RNAtranscripts capable of suppressing the expression of the target protein.

As stated herein, “suppression” refers to the reduction of the level ofenzyme activity or protein functionality detectable in a transgenicplant when compared to the level of enzyme activity or proteinfunctionality detectable in a plant with the native enzyme or protein.The level of enzyme activity in a plant with the native enzyme isreferred to herein as “wild type” activity. The level of proteinfunctionality in a plant with the native protein is referred to hereinas “wild type” functionality. The term “suppression” includes lower,reduce, decline, decrease, inhibit, eliminate and prevent. Thisreduction may be due to the decrease in translation of the native mRNAinto an active enzyme or functional protein. It may also be due to thetranscription of the native DNA into decreased amounts of mRNA and/or torapid degradation of the native mRNA. The term “native enzyme” refers toan enzyme that is produced naturally in the desired cell.

“Gene silencing,” as used herein, is a general term that refers todecreasing mRNA levels as compared to wild-type plants, does not specifymechanism and is inclusive, and not limited to, anti-sense,cosuppression, viral-suppression, hairpin suppression and stem-loopsuppression.

The terms “homology”, “homologous”, “substantially similar” and“corresponding substantially” are used interchangeably herein. Theyrefer to nucleic acid fragments wherein changes in one or morenucleotide bases does not affect the ability of the nucleic acidfragment to mediate gene expression or produce a certain phenotype.These terms also refer to modifications of the nucleic acid fragments ofthe instant invention such as deletion or insertion of one or morenucleotides that do not substantially alter the functional properties ofthe resulting nucleic acid fragment relative to the initial, unmodifiedfragment. For example, alterations in a nucleic acid fragment whichresult in the production of a chemically equivalent amino acid at agiven site, but do not effect the functional properties of the encodedpolypeptide, are well known in the art. Thus, a codon for the amino acidalanine, a hydrophobic amino acid, may be substituted by a codonencoding another less hydrophobic residue, such as glycine, or a morehydrophobic residue, such as valine, leucine, or isoleucine. Similarly,changes which result in substitution of one negatively charged residuefor another, such as aspartic acid for glutamic acid, or one positivelycharged residue for another, such as lysine for arginine, can also beexpected to produce a functionally equivalent product. Nucleotidechanges that result in alteration of the N-terminal and C-terminalportions of the polypeptide molecule would also not be expected to alterthe activity of the polypeptide. Each of the proposed modifications iswell within the routine skill in the art, as is determination ofretention of biological activity of the encoded products. It istherefore understood, as those skilled in the art will appreciate, thatthe invention encompasses more than the specific exemplary sequences.

Moreover, the skilled artisan recognizes that substantially similarnucleic acid sequences encompassed by this invention are also defined bytheir ability to hybridize, under moderately stringent conditions (forexample, 1×SSC, 0.1% SDS, 60° C.) with the sequences exemplified herein,or to any portion of the nucleotide sequences reported herein and whichare functionally equivalent to the gene or the promoter of theinvention. Stringency conditions can be adjusted to screen formoderately similar fragments, such as homologous sequences fromdistantly related organisms, to highly similar fragments, such as genesthat duplicate functional enzymes from closely related organisms.Post-hybridization washes determine stringency conditions. One set ofpreferred conditions involves a series of washes starting with 6×SSC,0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5%SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDSat 50° C. for 30 min. A more preferred set of stringent conditionsinvolves the use of higher temperatures in which the washes areidentical to those above except for the temperature of the final two 30min washes in 0.2×SSC, 0.5% SDS was increased to 60° C. Anotherpreferred set of highly stringent conditions involves the use of twofinal washes in 0.1×SSC, 0.1% SDS at 65° C.

With respect to the degree of substantial similarity between the target(endogenous) mRNA and the RNA region in the construct having homology tothe target mRNA, such sequences should be at least 25 nucleotides inlength, preferably at least 50 nucleotides in length, more preferably atleast 100 nucleotides in length, again more preferably at least 200nucleotides in length, and most preferably at least 300 nucleotides inlength; and should be at least 80% identical, preferably at least 85%identical, more preferably at least 90% identical, and most preferablyat least 95% identical.

Substantially similar nucleic acid fragments of the instant inventionmay also be characterized by the percent identity of the amino acidsequences that they encode to the amino acid sequences disclosed herein,as determined by algorithms commonly employed by those skilled in thisart. Suitable nucleic acid fragments (isolated polynucleotides of thepresent invention) encode polypeptides that are at least 70% identical,preferably at least 80% identical to the amino acid sequences reportedherein. Preferred nucleic acid fragments encode amino acid sequencesthat are at least 85% identical to the amino acid sequences reportedherein. More preferred nucleic acid fragments encode amino acidsequences that are at least 90% identical to the amino acid sequencesreported herein. Most preferred are nucleic acid fragments that encodeamino acid sequences that are at least 95% identical to the amino acidsequences reported herein.

It is well understood by one skilled in the art that many levels ofsequence identity are useful in identifying related polypeptidesequences. Useful examples of percent identities are 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 55% to100%.

Sequence alignments and percent similarity calculations may bedetermined using a variety of comparison methods designed to detecthomologous sequences including, but not limited to, the Megalign programof the LASARGENE bioinformatics computing suite (DNASTAR Inc., Madison,Wis.). Unless stated otherwise, multiple alignment of the sequencesprovided herein were performed using the Clustal method of alignment(Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters(GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwisealignments and calculation of percent identity of protein sequencesusing the Clustal method are KTUPLE=1, GAP PENALTY=3, WINDOW=5 andDIAGONALS SAVED=5. For nucleic acids these parameters are KTUPLE=2, GAPPENALTY=5, WINDOW=4 and DIAGONALS SAVED=4. After alignment of thesequences, using the Clustal V program, it is possible to obtain a“percent identity” by viewing the “sequence distances” table on the sameprogram.

Unless otherwise stated, “BLAST” sequence identity/similarity valuesprovided herein refer to the value obtained using the BLAST 2.0 suite ofprograms using default parameters (Altschul et al., Nucleic Acids Res.25:3389-3402 (1997)). Software for performing BLAST analyses is publiclyavailable, e.g., through the National Center for BiotechnologyInformation. This algorithm involves first identifying high scoringsequence pairs (HSPs) by identifying short words of length W in thequery sequence, which either match or satisfy some positive-valuedthreshold score T when aligned with a word of the same length in adatabase sequence. T is referred to as the neighborhood word scorethreshold (Altschul et al., supra). These initial neighborhood word hitsact as seeds for initiating searches to find longer HSPs containingthem. The word hits are then extended in both directions along eachsequence for as far as the cumulative alignment score can be increased.Cumulative scores are calculated using, for nucleotide sequences, theparameters M (reward score for a pair of matching residues; always>0)and N (penalty score for mismatching residues; always<0). For amino acidsequences, a scoring matrix is used to calculate the cumulative score.Extension of the word hits in each direction are halted when: thecumulative alignment score falls off by the quantity X from its maximumachieved value; the cumulative score goes to zero or below, due to theaccumulation of one or more negative-scoring residue alignments; or theend of either sequence is reached. The BLAST algorithm parameters W, T,and X determine the sensitivity and speed of the alignment. The BLASTNprogram (for nucleotide sequences) uses as defaults a wordlength (W) of11, an expectation (E) of 10, a cutoff of 100, M=5, N=⁻4, and acomparison of both strands. For amino acid sequences, the BLASTP programuses as defaults a wordlength (W) of 3, an expectation (E) of 10, andthe BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad.Sci. USA 89:10915 (1989)).

“Sequence identity” or “identity” in the context of nucleic acid orpolypeptide sequences refers to the nucleic acid bases or amino acidresidues in the two sequences that are the same when aligned for maximumcorrespondence over a specified comparison window.

Thus, “Percentage of sequence identity” refers to the valued determinedby comparing two optimally aligned sequences over a comparison window,wherein the portion of the polynucleotide sequence in the comparisonwindow may comprise additions or deletions (i.e., gaps) as compared tothe reference sequence (which does not comprise additions or deletions)for optimal alignment of the two sequences. The percentage is calculatedby determining the number of positions at which the identical nucleicacid base or amino acid residue occurs in both sequences to yield thenumber of matched positions, dividing the number of matched positions bythe total number of positions in the window of comparison andmultiplying the results by 100 to yield the percentage of sequenceidentity. Useful examples of percent sequence identities include, butare not limited to, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%,or any integer percentage from 55% to 100%. These identities can bedetermined using any of the programs described herein.

Sequence alignments and percent identity or similarity calculations maybe determined using a variety of comparison methods designed to detecthomologous sequences including, but not limited to, the Megalign programof the LASARGENE bioinformatics computing suite (DNASTAR Inc., Madison,Wis.). Multiple alignment of the sequences are performed using theClustal V method of alignment (Higgins, D. G. and Sharp, P. M. (1989)Comput. AppL Biosci. 5:151-153; Higgins, D. G. et al. (1992) Comput.AppL. Biosci. 8:189-191) with the default parameters (GAP PENALTY=10,GAP LENGTH PENALTY=10). Default parameters for pairwise alignments andcalculation of percent identity of protein sequences using the Clustalmethod are KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. Fornucleic acids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 andDIAGONALS SAVED=4.

It is well understood by one skilled in the art that many levels ofsequence identity are useful in identifying polypeptides, from otherplant species, wherein such polypeptides have the same or similarfunction or activity. Useful examples of percent identities include, butare not limited to, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%,or any integer percentage from 55% to 100%. Indeed, any integer aminoacid identity from 50%-100% may be useful in describing the presentinvention. Also, of interest is any full or partial complement of thisisolated nucleotide fragment.

The term “recombinant” means, for example, that a nucleic acid sequenceis made by an artificial combination of two otherwise separated segmentsof sequence, e.g., by chemical synthesis or by the manipulation ofisolated nucleic acids by genetic engineering techniques.

As used herein, “contig” refers to a nucleotide sequence that isassembled from two or more constituent nucleotide sequences that sharecommon or overlapping regions of sequence homology. For example, thenucleotide sequences of two or more nucleic acid fragments can becompared and aligned in order to identify common or overlappingsequences. Where common or overlapping sequences exist between two ormore nucleic acid fragments, the sequences (and thus their correspondingnucleic acid fragments) can be assembled into a single contiguousnucleotide sequence.

“Codon degeneracy” refers to divergence in the genetic code permittingvariation of the nucleotide sequence without affecting the amino acidsequence of an encoded polypeptide. Accordingly, the instant inventionrelates to any nucleic acid fragment comprising a nucleotide sequencethat encodes all or a substantial portion of the amino acid sequencesset forth herein. The skilled artisan is well aware of the “codon-bias”exhibited by a specific host cell in usage of nucleotide codons tospecify a given amino acid. Therefore, when synthesizing a nucleic acidfragment for improved expression in a host cell, it is desirable todesign the nucleic acid fragment such that its frequency of codon usageapproaches the frequency of preferred codon usage of the host cell.

The terms “synthetic nucleic acid” or “synthetic genes” refer to nucleicacid molecules assembled either in whole or in part from oligonucleotidebuilding blocks that are chemically synthesized using procedures knownto those skilled in the art. These building blocks are ligated andannealed to form larger nucleic acid fragments which may then beenzymatically assembled to construct the entire desired nucleic acidfragment. “Chemically synthesized”, as related to a nucleic acidfragment, means that the component nucleotides were assembled in vitro.Manual chemical synthesis of nucleic acid fragments may be accomplishedusing well established procedures, or automated chemical synthesis canbe performed using one of a number of commercially available machines.Accordingly, the nucleic acid fragments can be tailored for optimal geneexpression based on optimization of the nucleotide sequence to reflectthe codon bias of the host cell. The skilled artisan appreciates thelikelihood of successful gene expression if codon usage is biasedtowards those codons favored by the host. Determination of preferredcodons can be based on a survey of genes derived from the host cellwhere sequence information is available.

“Gene” refers to a nucleic acid fragment that is capable of directingexpression a specific protein or functional RNA.

“Native gene” refers to a gene as found in nature with its ownregulatory sequences.

“Chimeric gene” or “recombinant DNA construct” are used interchangeablyherein, and refers any gene that is not a native gene, comprisingregulatory and coding sequences that are not found together in nature,or to an isolated native gene optionally modified and reintroduced intoa host cell.

A chimeric gene may comprise regulatory sequences and coding sequencesthat are derived from different sources, or regulatory sequences andcoding sequences derived from the same source, but arranged in a mannerdifferent than that found in nature. In one embodiment, a regulatoryregion and a coding sequence region are assembled from two differentsources. In another embodiment, a regulatory region and a codingsequence region are derived from the same source but arranged in amanner different than that found in nature. In another embodiment, thecoding sequence region is assembled from at least two different sources.In another embodiment, the coding region is assembled from the samesource but in a manner not found in nature.

The term “endogenous gene” refers to a native gene in its naturallocation in the genome of an organism.

The term “foreign gene” refers to a gene not normally found in the hostorganism that is introduced into the host organism by gene transfer.

The term “transgene” refers to a gene that has been introduced into ahost cell by a transformation procedure. Transgenes may becomephysically inserted into a genome of the host cell (e.g., throughrecombination) or may be maintained outside of a genome of the host cell(e.g., on an extrachromasomal array).

An “allele” is one of several alternative forms of a gene occupying agiven locus on a chromosome. When the alleles present at a given locuson a pair of homologous chromosomes in a diploid plant are the same thatplant is homozygous at that locus. If the alleles present at a givenlocus on a pair of homologous chromosomes in a diploid plant differ thatplant is heterozygous at that locus. If a transgene is present on one ofa pair of homologous chromosomes in a diploid plant that plant ishemizygous at that locus.

The term “coding sequence” refers to a DNA fragment that codes for apolypeptide having a specific amino acid sequence, or a structural RNA.The boundaries of a protein coding sequence are generally determined bya ribosome binding site (prokaryotes) or by an ATG start codon(eukaryotes) located at the 5′ end of the mRNA and a transcriptionterminator sequence located just downstream of the open reading frame atthe 3′ end of the mRNA. A coding sequence can include, but is notlimited to, DNA, cDNA, and recombinant nucleic acid sequences.

“Mature” protein refers to a post-translationally processed polypeptide;i.e., one from which any pre- or pro-peptides present in the primarytranslation product have been removed. “Precursor” protein refers to theprimary product of translation of mRNA; i.e., with pre- and pro-peptidesstill present. Pre- and pro-peptides may be and are not limited tointracellular localization signals.

“RNA transcript” refers to the product resulting from RNApolymerase-catalyzed transcription of a DNA sequence. When the RNAtranscript is a perfect complementary copy of the DNA sequence, it isreferred to as the primary transcript or it may be a RNA sequencederived from post-transcriptional processing of the primary transcriptand is referred to as the mature RNA. “Messenger RNA (mRNA)” refers tothe RNA that is without introns and that can be translated into proteinby the cell. “cDNA” refers to a DNA that is complementary to andsynthesized from an mRNA template using the enzyme reversetranscriptase. The cDNA can be single-stranded or converted into thedouble-stranded form using the Klenow fragment of DNA polymerase I.“Sense” RNA refers to RNA transcript that includes the mRNA and can betranslated into protein within a cell or in vitro. “Antisense RNA”refers to an RNA transcript that is complementary to all or part of atarget primary transcript or mRNA and that blocks the expression of atarget isolated nucleic acid fragment (U.S. Pat. No. 5,107,065). Thecomplementarity of an antisense RNA may be with any part of the specificgene transcript, i.e., at the 5′ non-coding sequence, 3′ non-codingsequence, introns, or the coding sequence. “Functional RNA” refers toantisense RNA, ribozyme RNA, or other RNA that may not be translated butyet has an effect on cellular processes. The terms “complement” and“reverse complement” are used interchangeably herein with respect tomRNA transcripts, and are meant to define the antisense RNA of themessage.

The term “endogenous RNA” refers to any RNA which is encoded by anynucleic acid sequence present in the genome of the host prior totransformation with the recombinant construct of the present invention,whether naturally-occurring or non-naturally occurring, i.e., introducedby recombinant means, mutagenesis, etc.

The term “non-naturally occurring” means artificial, not consistent withwhat is normally found in nature.

“Messenger RNA (mRNA)” refers to the RNA that is without introns andthat can be translated into protein by the cell.

“cDNA” refers to a DNA that is complementary to and synthesized from amRNA template using the enzyme reverse transcriptase. The cDNA can besingle-stranded or converted into the double-stranded form using theKlenow fragment of DNA polymerase I.

“Sense” RNA refers to RNA transcript that includes the mRNA and can betranslated into protein within a cell or in vitro.

“Antisense RNA” refers to an RNA transcript that is complementary to allor part of a target primary transcript or mRNA, and that blocks theexpression of a target gene (U.S. Pat. No. 5,107,065). Thecomplementarity of an antisense RNA may be with any part of the specificgene transcript, i.e., at the 5′ non-coding sequence, 3′ non-codingsequence, introns, or the coding sequence.

“Functional RNA” refers to antisense RNA, ribozyme RNA, or other RNAthat may not be translated, yet has an effect on cellular processes. Theterms “complement” and “reverse complement” are used interchangeablyherein with respect to mRNA transcripts, and are meant to define theantisense RNA of the message.

The term “recombinant DNA construct” refers to a DNA construct assembledfrom nucleic acid fragments obtained from different sources. The typesand origins of the nucleic acid fragments may be very diverse.

A “recombinant expression construct” contains a nucleic acid fragmentoperably linked to at least one regulatory element, that is capable ofeffecting expression of the nucleic acid fragment. The recombinantexpression construct may also affect expression of a homologous sequencein a host cell.

In one embodiment the choice of recombinant expression construct isdependent upon the method that will be used to transform host cells. Theskilled artisan is well aware of the genetic elements that must bepresent on the recombinant expression construct in order to successfullytransform, select and propagate host cells. The skilled artisan willalso recognize that different independent transformation events may bescreened to obtain lines displaying the desired expression level andpattern. Such screening may be accomplished by, but is not limited to,Southern analysis of DNA, Northern analysis of mRNA expression, Westernanalysis of protein expression, or phenotypic analysis.

The term “operably linked” refers to the association of nucleic acidfragments on a single nucleic acid fragment so that the function of oneis regulated by the other. For example, a promoter is operably linkedwith a coding sequence when it is capable of regulating the expressionof that coding sequence (i.e., that the coding sequence is under thetranscriptional control of the promoter). Coding sequences can beoperably linked to regulatory sequences in a sense or antisenseorientation. In another example, the complementary RNA regions of theinvention can be operably linked, either directly or indirectly, 5′ tothe target mRNA, or 3′ to the target mRNA, or within the target mRNA, ora first complementary region is 5′ and its complement is 3′ to thetarget mRNA.

“Regulatory sequences” refer to nucleotides located upstream (5′non-coding sequences), within, or downstream (3′ non-coding sequences)of a coding sequence, and which may influence the transcription, RNAprocessing, stability, or translation of the associated coding sequence.Regulatory sequences may include, and are not limited to, promoters,translation leader sequences, introns, and polyadenylation recognitionsequences.

“Promoter” refers to a DNA sequence capable of controlling theexpression of a coding sequence or functional RNA. The promoter sequenceconsists of proximal and more distal upstream elements, the latterelements often referred to as enhancers. Accordingly, an “enhancer” is aDNA sequence which can stimulate promoter activity and may be an innateelement of the promoter or a heterologous element inserted to enhancethe level or tissue-specificity of a promoter. Promoter sequences canalso be located within the transcribed portions of genes, and/ordownstream of the transcribed sequences. Promoters may be derived intheir entirety from a native gene, or be composed of different elementsderived from different promoters found in nature, or even comprisesynthetic DNA segments. It is understood by those skilled in the artthat different promoters may direct the expression of an isolatednucleic acid fragment in different tissues or cell types, or atdifferent stages of development, or in response to differentenvironmental conditions. Promoters which cause an isolated nucleic acidfragment to be expressed in most cell types at most times are commonlyreferred to as “constitutive promoters”. New promoters of various typesuseful in plant cells are constantly being discovered; numerous examplesmay be found in the compilation by Okamuro and Goldberg, (1989)Biochemistry of Plants 15:1-82. It is further recognized that since inmost cases the exact boundaries of regulatory sequences have not beencompletely defined, DNA fragments of some variation may have identicalpromoter activity.

Specific examples of promoters that may be useful in expressing thenucleic acid fragments of the invention include, but are not limited to,the oleosin promoter (PCT Publication WO99/65479, published Dec. 12,1999), the maize 27kD zein promoter (Ueda et al (1994) Mol. Cell. Biol.14:4350-4359), the ubiquitin promoter (Christensen et al (1992) PlantMol. Biol. 18:675-680), the SAM synthetase promoter (PCT PublicationWO00/37662, published Jun. 29, 2000), the CaMV 35S (Odell et al (1985)Nature 313:810-812), and the promoter described in PCT PublicationWO02/099063 published Dec. 12, 2002.

The “translation leader sequence” refers to a polynucleotide fragmentlocated between the promoter of a gene and the coding sequence. Thetranslation leader sequence is present in the fully processed mRNAupstream of the translation start sequence. The translation leadersequence may affect processing of the primary transcript to mRNA, mRNAstability or translation efficiency. Examples of translation leadersequences have been described (Turner, R. and Foster, G. D. (1995) Mol.Biotechnol. 3:225-236).

An “intron” is an intervening sequence in a gene that does not encode aportion of the protein sequence. Thus, such sequences are transcribedinto RNA but are then excised and are not translated. The term is alsoused for the excised RNA sequences.

The “3′ non-coding sequences” refer to DNA sequences located downstreamof a coding sequence and include polyadenylation recognition sequencesand other sequences encoding regulatory signals capable of affectingmRNA processing or gene expression. The polyadenylation signal isusually characterized by affecting the addition of polyadenylic acidtracts to the 3′ end of the mRNA precursor. The use of different 3′non-coding sequences is exemplified by Ingelbrecht, I. L., et al. (1989)Plant Cell 1:671-680.

Standard recombinant DNA and molecular cloning techniques used hereinare well known in the art and are described more fully in Sambrook, J.,Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual;Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989.Transformation methods are well known to those skilled in the art andare described below.

“PCR” or “Polymerase Chain Reaction” is a technique for the synthesis oflarge quantities of specific DNA segments, consists of a series ofrepetitive cycles (Perkin Elmer Cetus Instruments, Norwalk, Conn.).Typically, the double stranded DNA is heat denatured, the two primerscomplementary to the 3′ boundaries of the target segment are annealed atlow temperature and then extended at an intermediate temperature. Oneset of these three consecutive steps is referred to as a cycle.

“Stable transformation” refers to the transfer of a nucleic acidfragment into a genome of a host organism, including nuclear andorganellar genomes, resulting in genetically stable inheritance.

In contrast, “transient transformation” refers to the transfer of anucleic acid fragment into the nucleus, or DNA-containing organelle, ofa host organism resulting in gene expression without integration orstable inheritance.

Host organisms comprising the transformed nucleic acid fragments arereferred to as “transgenic” organisms.

The term “amplified” means the construction of multiple copies of anucleic acid sequence or multiple copies complementary to the nucleicacid sequence using at least one of the nucleic acid sequences as atemplate. Amplification systems include the polymerase chain reaction(PCR) system, ligase chain reaction (LCR) system, nucleic acid sequencebased amplification (NASBA, Cangene, Mississauga, Ontario), Q-BetaReplicase systems, transcription-based amplification system (TAS), andstrand displacement amplification (SDA). See, e.g., Diagnostic MolecularMicrobiology: Principles and Applications, D. H. Persing et al., Ed.,American Society for Microbiology, Washington, D.C. (1993). The productof amplification is termed an amplicon.

The term “chromosomal location” includes reference to a length of achromosome which may be measured by reference to the linear segment ofDNA which it comprises. The chromosomal location can be defined byreference to two unique DNA sequences, i.e., markers.

The term “marker” includes reference to a locus on a chromosome thatserves to identify a unique position on the chromosome. A “polymorphicmarker” includes reference to a marker which appears in multiple forms(alleles) such that different forms of the marker, when they are presentin a homologous pair, allow transmission of each of the chromosomes inthat pair to be followed. A genotype may be defined by use of one or aplurality of markers.

The present invention includes, inter alia, compositions and methods formodulating (i.e., increasing or decreasing) the level of plastidicpolypeptides described herein in plants. The size of the starch andsoluble carbohydrate pools in soybean seeds can be modulated by alteringthe expression of a specific gene, encoding plastidic phosphoglucomutase(pPGM), which is involved in the starch and soluble carbohydratebiosynthetic pathway.

Silencing of pPGM gene expression in transgenic soybeans seeds resultedin a drastic decrease of the transient starch pool accompanied by areduction in soluble carbohydrates and a concomitant increase incombined oil and protein content. Elimination of the transient starchpool by silencing plastidic PGM gene expression in soybean seedsdiverted carbon away from the soluble carbohydrate components of drysoybean seeds with the major decrease occurring in the sucrose pool.This is in contrast to PGM mutants of pea, Arabidopsis, and Nicotiana,where the carbon is mainly funneled into the soluble carbohydrate pool.

The data discussed below further indicates that soybean seeds deficientin plastidic PGM reallocate the carbon destined for starch biosynthesistoward the biosynthesis oil and protein and also alters the sucrose toraffinose family oligosaccharide ratio.

In contrast, a 40% reduction in storage lipid content was observed inthe Arabidopsis mutant pgm-1, which contains a point mutation in theAtPGM gene rendering the polypeptide nonfunctional (Periappuram et al.,(2000) Plant Physiol. 122:1193-1199).

An alteration of plastidic PGM activity affects the allocation of carbonto the soluble carbohydrate pool as well as the allocation of carbon tooil and protein biosynthesis. This is accomplished with no adverseeffect on plant and seed phenotype. Since all known soybean cultivarscontain transient starch, silencing the plastidic PGM gene in anysoybean cultivar should result in a decrease of the transient carbonreserve together with an increase in the combined oil and protein level.This increase in the combined oil and protein level is in addition tothe oil and protein levels of the wild-type genotype, regardless ofwhether the level is low or high. For example, a soybean variety such asSakaii-18 has 56% of its seed dry weight as protein and 14% as oil. APioneer soybean variety, 9306, contains 41% protein and 23% oil (as seeddry weight). Both genotypes would be expected to have an increase in thecombined oil and protein content as well as altered sucrose to raffinosefamily oligosaccharide ratio.

In one embodiment, the present invention concerns an isolatedpolynucleotide comprising: (a) a first nucleotide sequence encoding afirst polypeptide comprising at least 560 amino acids, wherein the aminoacid sequence of the first polypeptide and the amino acid sequence ofSEQ ID NO:8 have at least 95%, 96%, 97%, 98%, 99% or 100% sequenceidentity, based on the Clustal V method of alignment, (b) a secondnucleotide sequence encoding a second polypeptide comprising at least560 amino acids, wherein the amino acid sequence of the secondpolypeptide and the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, orSEQ ID NO:10 have at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100%sequence identity, based on the Clustal V method of alignment, or (c)the complement of the first or second nucleotide sequence, wherein thecomplement and the first or second nucleotide sequence contain the samenumber of nucleotides and are 100% complementary. The first polypeptidepreferably comprises the amino acid sequence of SEQ ID NO:8, and thesecond polypeptide preferably comprises the amino acid sequence of SEQID NO:2, SEQ ID NO:4, or SEQ ID NO:10. The first nucleotide sequencepreferably comprises the nucleotide sequence of SEQ ID NO:7, the secondnucleotide sequence preferably comprises the nucleotide sequence of SEQID NO:1, SEQ ID NO:3, or SEQ ID NO:9. The first and second polypeptidespreferably have phosphoglucomutase activity.

In another embodiment, the present invention relates to a recombinantDNA construct comprising any of the isolated polynucleotides of thepresent invention operably linked to at least one regulatory sequence.

In another preferred embodiment of the present invention, a recombinantDNA construct of the present invention further comprises an enhancer.

In another embodiment, the present invention relates to a vectorcomprising any of the isolated polynucleotides of the present invention.

In another embodiment, the present invention relates to an isolatedpolynucleotide fragment comprising a nucleotide sequence comprised byany of the polynucleotides of the present invention, wherein thenucleotide sequence contains at least 30, 40, 60, 100, 200, 300, 400,500 or 541 nucleotides.

In another embodiment, the present invention relates to a method fortransforming a cell comprising transforming a cell with any of theisolated polynucleotides of the present invention, and the celltransformed by this method. Advantageously, the cell is eukaryotic,e.g., a yeast or plant cell, or prokaryotic, e.g., a bacterium.

In another embodiment, the present invention relates to a method fortransforming a cell, comprising transforming a cell with apolynucleotide of the present invention.

In another embodiment, the present invention relates to a method forproducing a transgenic plant comprising transforming a plant cell withany of the isolated polynucleotides of the present invention andregenerating a transgenic plant from the transformed plant cell.

In another embodiment, a cell, plant, or seed comprising a recombinantDNA construct of the present invention.

In another embodiment, the present invention concerns an isolatedpolypeptide comprising: (a) a first amino acid sequence comprising atleast 560 amino acids, wherein the first amino acid sequence and theamino acid sequence of SEQ ID NO:8 have at least 95%, 96%, 97%, 98%, 99%or 100% sequence identity, based on the Clustal V method of alignment,and (b) a second amino acid sequence comprising at least 560 aminoacids, wherein the second amino acid sequence and the amino acidsequence of SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:10 have at least 85%,90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity, based on theClustal V method of alignment. The first amino acid sequence preferablycomprises the amino acid sequence of SEQ ID NO:8, and the second aminoacid sequence preferably comprises the amino acid sequence SEQ ID NO:2,SEQ ID NO:4, or SEQ ID NO:10. The polypeptide preferably hasphosphoglucomutase activity.

In another embodiment, the present invention relates to a virus,preferably a baculovirus, comprising any of the isolated polynucleotidesof the present invention or any of the recombinant DNA constructs of thepresent invention.

In another embodiment, the invention relates to a method of selecting anisolated polynucleotide that alters, i.e., increases or decreases, thelevel of expression of a phosphoglucomutase gene, protein or enzymeactivity in a host cell, preferably a plant cell, the method comprisingthe steps of: (a) constructing an isolated polynucleotide of the presentinvention or an isolated recombinant DNA construct of the presentinvention; (b) introducing the isolated polynucleotide or the isolatedrecombinant DNA construct into a host cell; (c) measuring the level ofthe phosphoglucomutase RNA, protein or enzyme activity in the host cellcontaining the isolated polynucleotide or recombinant DNA construct; (d)comparing the level of the phosphoglucomutase RNA, protein or enzymeactivity in the host cell containing the isolated polynucleotide orrecombinant DNA construct with the level of the phosphoglucomutase RNA,protein or enzyme activity in a host cell that does not contain theisolated polynucleotide or recombinant DNA construct, and selecting theisolated polynucleotide or recombinant DNA construct that alters, i.e.,increases or decreases, the level of expression of thephosphoglucomutase gene, protein or enzyme activity in the plant cell.

In another embodiment, the invention concerns a method of obtaining anucleic acid fragment encoding a substantial portion of aphosphoglucomutase protein, preferably a plant phosphoglucomutaseprotein, comprising the steps of: synthesizing an oligonucleotide primercomprising a nucleotide sequence of at least 30 contiguous nucleotides,preferably at least 40 contiguous nucleotides, more preferably at least60 contiguous nucleotides derived from a nucleotide sequence selectedfrom the group consisting of SEQ ID NOs:1, 3, 5, 7, and 9, and thecomplement of such nucleotide sequences; and amplifying a nucleic acidfragment (preferably a cDNA inserted in a cloning vector) using theoligonucleotide primer. The amplified nucleic acid fragment preferablywill encode a substantial portion of a phosphoglucomutase protein aminoacid sequence.

In another embodiment, the invention relates to a method of obtaining anucleic acid fragment encoding all or a substantial portion of the aminoacid sequence encoding a phosphoglucomutase protein comprising the stepsof: probing a cDNA or genomic library with an isolated polynucleotide ofthe present invention; identifying a DNA clone that hybridizes with anisolated polynucleotide of the present invention; isolating theidentified DNA clone; and sequencing the cDNA or genomic fragment thatcomprises the isolated DNA clone.

In another embodiment, the invention concerns a method for positiveselection of a transformed cell comprising: (a) transforming a host cellwith the recombinant DNA construct of the present invention or anexpression cassette of the present invention; and (b) growing thetransformed host cell, preferably a plant cell, such as a monocot or adicot, under conditions which allow expression of the phosphoglucomutasepolynucleotide in an amount sufficient to complement a null mutant toprovide a positive selection means.

In another embodiment, this invention concerns a method for suppressingthe level of expression of a gene encoding a plastidic polypeptidehaving phosphoglucomutase activity in a transgenic plant, wherein themethod comprises:

-   -   (a) transforming a plant cell with a fragment of the isolated        polynucleotide of the invention;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant wherein the level of expression        of a gene encoding a plastidic polypeptide having        phosphoglucomutase activity has been suppressed.

Preferably, the gene encodes a plastidic polypeptide havingphosphoglucomutase activity, and the plant is a soybean plant.

In another embodiment, the invention concerns a recombinant DNAconstruct comprising: (a) all or part of the nucleotide sequence setforth in SEQ ID NO:7 or SEQ ID NO:15; or (b) the complement of (a);wherein (a) or (b) is useful in cosuppression or antisense suppressionof endogenous phosphoglucomutase activity in a transgenic plant.

In another embodiment, the invention concerns a method for producingtransgenic seed, the method comprising:

-   -   (a) transforming a plant cell with the recombinant DNA construct        of    -   (i) all or part of the nucleotide sequence set forth in SEQ ID        NO:7 or SEQ ID NO:15; or    -   (ii) the complement of (i);

wherein (i) or (ii) is useful in co-suppression or antisense suppressionof endogenous phosphoglucomutase activity in a transgenic plant;

-   -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        having an increase in the combined oil and protein content of at        least 1.6% and a decrease in the sucrose content of at least 25%        as compared to seed obtained from a non-transgenic plant.        Preferably, the seed is a soybean seed.

In another embodiment, the invention concerns a method method forproducing transgenic seed, the method comprising:

-   -   (a) transforming a plant cell with a recombinant DNA construct        comprising    -   (i) all or part of the nucleotide sequence set forth in SEQ ID        NO:7 or SEQ ID NO:15; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous phosphoglucomutase activity in a        transgenic plant;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        having a sucrose to raffinose family oligosaccharide ratio of        1.0 or less as compared to seed obtained from a non-transgenic        plant.

Preferably, the transgenic seed differs from an untransformed seed byhaving an increase in the combined oil and protein content of at least1.6%, 1.8% or 2.0%. Preferably, the seed is a soybean seed.

In another embodiment, the invention concerns a method for producingdefatted meal from transgenic seed, comprising:

-   -   (a) transforming a plant cell with a recombinant DNA construct        comprising (i) all or part of the nucleotide sequence set forth        in SEQ ID NO:7 or SEQ ID NO:15; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous phosphoglucomutase activity in a        transgenic plant;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        wherein said seed is processed into defatted meal having an        increase in the combined oil and protein content of at least 5%        and a decrease in the sucrose content of at least 25% as        compared to defatted meal obtained from seed of a non-transgenic        plant.

Preferably, the defatted meal of the transgenic seed differs from thedefatted meal of an untransformed seed by having a sucrose to raffinosefamily oligosaccharide ratio of 1.0 or less. Preferably, the seed is asoybean seed.

In a another embodiment, the invention concerns a transgenic seed thatdiffers from an non-transgenic seed by having an increase in thecombined oil and protein content of at least 1.6%, 1.8% or 2.0%, and adecrease in the sucrose content of at least 25%. Preferably, the seed isa soybean seed.

In another embodiment, the invention concerns a transgenic seed thatdiffers from non-transgenic seed by having a sucrose to raffinose familyoligosaccharide ratio of 1.0 or less. Preferably, the transgenic seeddiffers from an untransformed seed by having an increase in the combinedoil and protein content of at least 1.6%, 1.8% or 2.0%. Preferably, theseed is a soybean seed.

In another embodiment, the invention concerns a transgenic seedcomprising

-   -   a recombinant construct comprising (i) all or part of the        nucleotide sequence set forth in SEQ ID NO:7 or SEQ ID NO:15; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous phosphoglucomutase activity in a        transgenic plant;    -   further wherein said transgenic seed is processed to make        defatted meal having an increase in the combined oil and protein        content of at least 5% and a decrease in the sucrose content of        at least 25% when compared to defatted meal obtained from a        non-transgenic seed.

Preferably, the defatted meal of the transgenic seed differs from thedefatted meal of an untransformed seed by having a sucrose to raffinosefamily oligosaccharide ratio of 1.0 or less. Preferably, the seed is asoybean seed.

Soybeans can be processed into a number of products. For example, “soyprotein products” can include, and are not limited to, those itemslisted in Table A. “Soy protein products”. TABLE A Soy Protein ProductsDerived from Soybean Seeds^(a) Processed Soy Protein Products WholeSoybean Products Roasted Soybeans Full Fat and Defatted Flours BakedSoybeans Soy Grits Soy Sprouts Soy Hypocotyls Soy Milk Soybean Meal SoyMilk Soy Protein Isolates Specialty Soy Foods/Ingredients Soy Milk SoyProtein Concentrates Tofu Textured Soy Proteins Tempeh Textured Floursand Concentrates Miso Textured Concentrates Soy Sauce Textured IsolatesHydrolyzed Vegetable Protein Whipping Protein^(a)See Soy Protein Products: Characteristics, Nutritional Aspects andUtilization (1987). Soy Protein Council.

“Processing” refers to any physical and chemical methods used to obtainthe products listed in Table A and includes, and is not limited to, heatconditioning, flaking and grinding, extrusion, solvent extraction, oraqueous soaking and extraction of whole or partial seeds. Furthermore,“processing” includes the methods used to concentrate and isolate soyprotein from whole or partial seeds, as well as the various traditionalOriental methods in preparing fermented soy food products. TradingStandards and Specifications have been established for many of theseproducts (see National Oilseed Processors Association Yearbook andTrading Rules 1991-1992).

“White” flakes refer to flaked, dehulled cotyledons that have beendefatted and treated with controlled moist heat to have a PDI (ASCS:ba10-65) of about 85 to 90. This term can also refer to a flour with asimilar PDI that has been ground to pass through a No. 100 U.S. StandardScreen size.

“Grits” refer to defatted, dehulled cotyledons having a U.S. Standardscreen size of between No. 10 and 80.

“Soy Protein Concentrates” refer to those products produced fromdehulled, defatted soybeans by three basic processes: acid leaching (atabout pH 4.5), extraction with alcohol (about 55-80%), and denaturingthe protein with moist heat prior to extraction with water. Conditionstypically used to prepare soy protein concentrates have been describedby Pass ((1975) U.S. Pat. No. 3,897,574; Campbell et al., (1985) in NewProtein Foods, ed. by Altschul and Wilcke, Academic Press, Vol. 5,Chapter 10, Seed Storage Proteins, pp 302-338).

“Extrusion” refers to processes whereby material (grits, flour orconcentrate) is passed through a jacketed auger using high pressures andtemperatures as a means of altering the texture of the material.“Texturing” and “structuring” refer to extrusion processes used tomodify the physical characteristics of the material. The characteristicsof these processes, including thermoplastic extrusion, have beendescribed previously (Atkinson (1970) U.S. Pat. No. 3,488,770, Horan(1985) In New Protein Foods, ed. by Altschul and Wilcke, Academic Press,Vol. 1A, Chapter 8, pp 367-414). Moreover, conditions used duringextrusion processing of complex foodstuff mixtures that include soyprotein products have been described previously (Rokey (1983) FeedManufacturing Technology III, 222-237; McCulloch, U.S. Pat. No.4,454,804).

In another embodiment, this invention concerns a method for suppressingthe level of expression of a gene encoding a polypeptide havingADP-glucose pyrophosphorylase activity in a transgenic plant, whereinthe method comprises:

-   -   (a) transforming a plant cell with a fragment SEQ ID NOs:24, 28        or 30, or their complement;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant wherein the level of expression        of a gene encoding a polypeptide having ADP-glucose        pyrophosphorylase activity has been suppressed.

Preferably, the plant is a soybean plant.

In another embodiment, the invention concerns a recombinant DNAconstruct comprising: (a) all or part of the nucleotide sequence setforth in SEQ ID NOs:24, 28 or 30; or (b) the complement of (a); wherein(a) or (b) is useful in co-suppression or antisense suppression ofendogenous ADP-glucose pyrophosphorylase activity in a transgenic plant.

In another embodiment, the invention concerns a method for producingtransgenic seed, the method comprising:

-   -   (a) transforming a plant cell with the recombinant DNA construct        of:    -   (i) all or part of the nucleotide sequence set forth in SEQ ID        NO:24, 28 or 30; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous ADP-glucose pyrophosphorylase activity        in a transgenic plant;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        having an increase in the combined oil and protein content of at        least 1.6% and a decrease in the sucrose content of at least 25%        as compared to seed obtained from a non-transgenic plant.

Preferably, the seed is a soybean seed.

In another embodiment, the invention concerns a method for producingtransgenic seed, the method comprising:

-   -   (a) transforming a plant cell with a recombinant DNA construct        comprising    -   (i) all or part of the nucleotide sequence set forth in SEQ ID        NOs:24, 28 or 30; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous ADP-glucose pyrophosphorylase activity        in a transgenic plant;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        having a sucrose to raffinose family oligosaccharide ratio of        1.0 or less as compared to seed obtained from a non-transgenic        plant.

Preferably, the transgenic seed differs from an untransformed seed byhaving an increase in the combined oil and protein content of at least1.6%, 1.8% or 2.0%. Preferably, the seed is a soybean seed.

In another embodiment, the invention concerns a method for producingdefatted meal from transgenic seed, comprising:

-   -   (a) transforming a plant cell with a recombinant DNA construct        comprising    -   (i) all or part of the nucleotide sequence set forth in SEQ ID        NOs:24, 28 or 30; or    -   (ii) the complement of (i);    -   wherein (i) or (ii) is useful in co-suppression or antisense        suppression of endogenous ADP-glucose pyrophosphorylase activity        in a transgenic plant;    -   (b) regenerating a transgenic plant from the transformed plant        cell of (a); and    -   (c) selecting a transgenic plant that produces a transgenic seed        wherein said seed is processed into defatted meal having an        increase in the combined oil and protein content of at least 5%        and a decrease in the sucrose content of at least 25% as        compared to defatted meal obtained from seed of a non-transgenic        plant.

Preferably, the defatted meal of the transgenic seed differs from thedefatted meal of an untransformed seed by having a sucrose to raffinosefamily oligosaccharide ratio of 1.0 or less. Preferably, the seed is asoybean seed.

In a another embodiment, the invention concerns a transgenic seedproduced by any of the above methods. Preferably, the seed is a soybeanseed.

Regulatory sequences may include, and are not limited to, promoters,translation leader sequences, introns, and polyadenylation recognitionsequences.

“Tissue-specific” promoters direct RNA production preferentially inparticular types of cells or tissues. Promoters which cause a gene to beexpressed in most cell types at most times are commonly referred to as“constitutive promoters”. New promoters of various types useful in plantcells are constantly being discovered; numerous examples may be found inthe compilation by Okamuro and Goldberg (Biochemistry of Plants 15:1-82(1989)). It is further recognized that since in most cases the exactboundaries of regulatory sequences have not been completely defined, DNAfragments of some variation may have identical promoter activity.

A number of promoters can be used to practice the present invention. Thepromoters can be selected based on the desired outcome. The nucleicacids can be combined with constitutive, tissue-specific (preferred),inducible, or other promoters for expression in the host organism.Suitable constitutive promoters for use in a plant host cell include,for example, the core promoter of the Rsyn7 promoter and otherconstitutive promoters disclosed in WO 99/43838 and U.S. Pat. No.6,072,050; the core CaMV 35S promoter (Odell et al., Nature 313:810-812(1985)); rice actin (McElroy et al., Plant Cell 2:163-171 (1990));ubiquitin (Christensen et al., Plant Mol. Biol. 12:619-632 (1989) andChristensen et al., Plant Mol. Biol. 18:675-689 (1992)); pEMU (Last etal., Theor. Appl. Genet. 81:581-588 (1991)); MAS (Velten et al., EMBO J.3:2723-2730 (1984)); ALS promoter (U.S. Pat. No. 5,659,026), and thelike. Other constitutive promoters include, for example, those discussedin U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785;5,399,680; 5,268,463; 5,608,142; and 6,177,611.

In choosing a promoter to use in the methods of the invention, it may bedesirable to use a tissue-specific or developmentally regulatedpromoter. A tissue-specific or developmentally regulated promoter is aDNA sequence which regulates the expression of a DNA sequenceselectively in particular cells/tissues of a plant. Any identifiablepromoter may be used in the methods of the present invention whichcauses the desired temporal and spatial expression.

Promoters which are seed or embryo specific and may be useful in theinvention include patatin (potato tubers) (Rocha-Sosa, M., et al. (1989)EMBO J. 8:23-29), convicilin, vicilin, and legumin (pea cotyledons)(Rerie, W. G., et al. (1991) Mol. Gen. Genet. 259:149-157; Newbigin, E.J., et al. (1990) Planta 180:461-470; Higgins, T. J. V., et al. (1988)Plant. Mol. Biol. 11:683-695), zein (maize endosperm) (Schemthaner, J.P., et al. (1988) EMBO J. 7:1249-1255), phaseolin (bean cotyledon)(Segupta-Gopalan, C., et al. (1985) Proc. Natl. Acad. Sci. U.S.A.82:3320-3324), phytohemagglutinin (bean cotyledon) (Voelker, T. et al.(1987) EMBO J. 6:3571-3577), B-conglycinin and glycinin (soybeancotyledon) (Chen, Z-L, et al. (1988) EMBO J. 7:297-302), glutelin (riceendosperm), hordein (barley endosperm) (Marris, C., et al. (1988) PlantMol. Biol. 10:359-366), glutenin and gliadin (wheat endosperm) (Colot,V., et al. (1987) EMBO J. 6:3559-3564), and sporamin (sweet potatotuberous root) (Hattori, T., et al. (1990) Plant Mol. Biol. 14:595-604).Promoters of seed-specific genes operably linked to heterologous codingregions in chimeric gene constructions maintain their temporal andspatial expression pattern in transgenic plants. Such examples includeArabidopsis thaliana 2S seed storage protein gene promoter to expressenkephalin peptides in Arabidopsis and Brassica napus seeds(Vanderkerckhove et al., Bio/Technology 7:L929-932 (1989)), bean lectinand bean beta-phaseolin promoters to express luciferase (Riggs et al.,Plant Sci. 63:47-57 (1989)), and wheat glutenin promoters to expresschloramphenicol acetyl transferase (Colot et al., EMBO J 6:3559-3564(1987)).

A plethora of promoters is described in WO 00/18963, published on Apr.6, 2000, the disclosure of which is hereby incorporated by reference.Examples of seed-specific promoters include, and are not limited to, thepromoter for soybean Kunitz trypsin inhibitor (Kti3, Jofuku andGoldberg, Plant Cell 1:1079-1093 (1989)) β-conglycinin (Chen et al.,Dev. Genet. 10:112-122 (1989)), the napin promoter, and the phaseolinpromoter.

In some embodiments, isolated nucleic acids which serve as promoter orenhancer elements can be introduced in the appropriate position(generally upstream) of a non-heterologous form of a polynucleotide ofthe present invention so as to up or down regulate expression of apolynucleotide of the present invention. For example, endogenouspromoters can be altered in vivo by mutation, deletion, and/orsubstitution (see, Kmiec, U.S. Pat. No. 5,565,350; Zarling et al.,PCT/US93/03868), or isolated promoters can be introduced into a plantcell in the proper orientation and distance from a cognate gene of apolynucleotide of the present invention so as to control the expressionof the gene. Gene expression can be modulated under conditions suitablefor plant growth so as to alter the total concentration and/or alter thecomposition of the polypeptides of the present invention in plant cell.Thus, the present invention includes compositions, and methods formaking, heterologous promoters and/or enhancers operably linked to anative, endogenous (i.e., non-heterologous) form of a polynucleotide ofthe present invention.

An intron sequence can be added to the 5′ untranslated region or thecoding sequence of the partial coding sequence to increase the amount ofthe mature message that accumulates in the cytosol. Inclusion of aspliceable intron in the transcription unit in both plant and animalexpression constructs has been shown to increase gene expression at boththe mRNA and protein levels up to 1000-fold (Buchman and Berg, Mol. CellBiol. 8:4395-4405 (1988); Callis et al., Genes Dev. 1:1183-1200 (1987)).Such intron enhancement of gene expression is typically greatest whenplaced near the 5′ end of the transcription unit. Use of maize intronsAdh1-S intron 1, 2, and 6, the Bronze-1 intron are known in the art. Seegenerally, The Maize Handbook, Chapter 116, Freeling and Walbot, Eds.,Springer, N.Y. (1994). A vector comprising the sequences from apolynucleotide of the present invention will typically comprise a markergene which confers a selectable phenotype on plant cells. Typicalvectors useful for expression of genes in higher plants are well knownin the art and include vectors derived from the tumor-inducing (Ti)plasmid of Agrobacterium tumefaciens described by Rogers et al., Meth.in Enzymol. 153:253-277 (1987).

If polypeptide expression is desired, it is generally desirable toinclude a polyadenylation region at the 3′-end of a polynucleotidecoding region. The polyadenylation region can be derived from thenatural gene, from a variety of other plant genes, or from T-DNA. The 3′end sequence to be added can be derived from, for example, the nopalinesynthase or octopine synthase genes, or alternatively from another plantgene, or less preferably from any other eukaryotic gene.

Preferred recombinant DNA constructs include the following combinations:a) a nucleic acid fragment corresponding to a promoter operably linkedto at least one nucleic acid fragment encoding a selectable marker,followed by a nucleic acid fragment corresponding to a terminator, b) anucleic acid fragment corresponding to a promoter operably linked to anucleic acid fragment capable of producing a stem-loop structure, andfollowed by a nucleic acid fragment corresponding to a terminator, andc) any combination of a) and b) above. Preferably, in the stem-loopstructure at least one nucleic acid fragment that is capable ofsuppressing expression of a native gene comprises the “loop” and issurrounded by nucleic acid fragments capable of producing a stem.

Preferred methods for transforming dicots and obtaining transgenicplants have been published, among others, for cotton (U.S. Pat. No.5,004,863, U.S. Pat. No. 5,159,135); soybean (U.S. Pat. No. 5,569,834,U.S. Pat. No. 5,416,011); Brassica (U.S. Pat. No. 5,463,174); peanut(Cheng et al. (1996) Plant Cell Rep. 15:653-657, McKently et al. (1995)Plant Cell Rep. 14:699-703); papaya (Ling, K. et al. (1991)Bio/technology 9:752-758); and pea (Grant et al. (1995) Plant Cell Rep.15:254-258). For a review of other commonly used methods of planttransformation see Newell, C. A. (2000) Mol. Biotechnol. 16:53-65. Oneof these methods of transformation uses Agrobacterium rhizogenes(Tepfler, M. and Casse-Delbart, F. (1987) Microbiol. Sci. 4:24-28).Transformation of soybeans using direct delivery of DNA has beenpublished using PEG fusion (PCT publication WO 92/17598),electroporation (Chowrira, G. M. et al. (1995) Mol. Biotechnol. 3:17-23;Christou, P. et al. (1987) Proc. Natl. Acad. Sci. U.S.A. 84:3962-3966),microinjection, or particle bombardment (McCabe, D. E. et. Al. (1988)BiolTechnology 6:923; Christou et al. (1988) Plant Physiol. 87:671-674).

There are a variety of methods for the regeneration of plants from planttissue. The particular method of regeneration will depend on thestarting plant tissue and the particular plant species to beregenerated. The regeneration, development and cultivation of plantsfrom single plant protoplast transformants or from various transformedexplants are well known in the art (Weissbach and Weissbach, (1988) In.:Methods for Plant Molecular Biology, (Eds.), Academic Press, Inc., SanDiego, Calif.). This regeneration and growth process typically includesthe steps of selection of transformed cells, culturing thoseindividualized cells through the usual stages of embryonic developmentthrough the rooted plantlet stage. Transgenic embryos and seeds aresimilarly regenerated. The resulting transgenic rooted shoots arethereafter planted in an appropriate plant growth medium such as soil.The regenerated plants may be self-pollinated. Otherwise, pollenobtained from the regenerated plants is crossed to seed-grown plants ofagronomically important lines. Conversely, pollen from plants of theseimportant lines is used to pollinate regenerated plants. A transgenicplant of the present invention containing a desired polypeptide(s) iscultivated using methods well known to one skilled in the art.

In addition to the above discussed procedures, practitioners arefamiliar with the standard resource materials which describe specificconditions and procedures for the construction, manipulation andisolation of macromolecules (e.g., DNA molecules, plasmids, etc.),generation of recombinant DNA fragments and recombinant expressionconstructs and the screening and isolating of clones, (see for example,Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Press; Maliga et al. (1995) Methods in Plant MolecularBiology, Cold Spring Harbor Press; Birren et al. (1998) Genome Analysis:Detecting Genes, 1, Cold Spring Harbor, N.Y.; Birren et al. (1998)Genome Analysis: Analyzing DNA, 2, Cold Spring Harbor, N.Y.; PlantMolecular Biology: A Laboratory Manual, eds. Clark, Springer, N.Y.(1997)).

Assays to detect proteins may be performed by SDS-polyacrylamide gelelectrophoresis or immunological assays. Assays to detect levels ofsubstrates or products of enzymes may be performed using gaschromatography or liquid chromatography for separation and UV or visiblespectrometry or mass spectrometry for detection, or the like.Determining the levels of mRNA of the enzyme of interest may beaccomplished using northern-blotting or RT-PCR techniques. Once plantshave been regenerated, and progeny plants homozygous for the transgenehave been obtained, plants will have a stable phenotype that will beobserved in similar seeds in later generations.

In another aspect, this invention includes a polynucleotide of thisinvention or a functionally equivalent subfragment thereof useful inantisense inhibition or cosuppression of expression of nucleic acidsequences encoding proteins having plastidic phosphoglucomutaseactivity, most preferably in antisense inhibition or cosuppression of anendogenous plastidic phosphoglucomutase gene.

Protocols for antisense inhibition or co-suppression are well known tothose skilled in the art.

Cosuppression constructs in plants have been previously designed byfocusing on overexpression of a nucleic acid sequence having homology toa native mRNA, in the sense orientation, which results in the reductionof all RNA having homology to the overexpressed sequence (see Vaucheretet al. (1998) Plant J. 16:651-659; and Gura (2000) Nature 404:804-808).Another variation describes the use of plant viral sequences to directthe suppression of proximal mRNA encoding sequences (PCT Publication WO98/36083 published on Aug. 20, 1998). Recent work has described the useof “hairpin” structures that incorporate all, or part, of an mRNAencoding sequence in a complementary orientation that results in apotential “stem-loop” structure for the expressed RNA (PCT PublicationWO 99/53050 published on Oct. 21, 1999). In this case the stem is formedby polynucleotides corresponding to the gene of interest inserted ineither sense or anti-sense orientation with respect to the promoter andthe loop is formed by some polynucleotides of the gene of interest,which do not have a complement in the construct. This increases thefrequency of cosuppression or silencing in the recovered transgenicplants. For review of hairpin suppression see Wesley, S. V. et al.(2003) Methods in Molecular Biology, Plant Functional Genomics: Methodsand Protocols 236:273-286. A construct where the stem is formed by atleast 30 nucleotides from a gene to be suppressed and the loop is formedby a random nucleotide sequence has also effectively been used forsuppression (WO 99/61632 published on Dec. 2, 1999). The use of poly-Tand poly-A sequences to generate the stem in the stem-loop structure hasalso been described (WO 02/00894 published Jan. 3, 2002). Yet anothervariation includes using synthetic repeats to promote formation of astem in the stem-loop structure. Transgenic organisms prepared with suchrecombinant DNA fragments have been shown to have reduced levels of theprotein encoded by the nucleotide fragment forming the loop as describedin PCT Publication WO 02/00904, published 3 Jan. 2002.

The sequences of the polynucleotide fragments used for suppression donot have to be 100% identical to the sequences of the polynucleotidefragment found in the gene to be suppressed. For example, suppression ofall the subunits of the soybean seed storage protein β-conglycinin hasbeen accomplished using a polynucleotide derived from a portion of thegene encoding the a subunit (U.S. Pat. No. 6,362,399). β-conglycinin isa heterogeneous glycoprotein composed of varying combinations of threehighly negatively charged subunits identified as α, α′ and β. Thepolynucleotide sequences encoding the α and α′ subunits are 85%identical to each other while the polynucleotide sequences encoding theβ subunit are 75 to 80% identical to the α and α′ subunits,respectively. Thus, polynucleotides that are at least 75% identical to aregion of the polynucleotide that is target for suppression have beenshown to be effective in suppressing the desired target. Thepolynucleotide may be at least 80% identical, at least 90% identical, atleast 95% identical, or about 100% identical to the desired targetsequence.

The isolated nucleic acids and proteins and any embodiments of thepresent invention can be used over a broad range of plant types,particularly dicots such as the species of the genus Glycine.

It is believed that the nucleic acids and proteins and any embodimentsof the present invention can be with monocots as well including, but notlimited to, Graminiae including Sorghum bicolor and Zea mays.

The isolated nucleic acid and proteins of the present invention can alsobe used in species from the following dicot genera: Cucurbita, Rosa,Vitis, Juglans, Fragaria, Lotus, Medicago, Onobrychis, Trifolium,Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus,Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura,Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis,Majorana, Cichorium, Helianthus, Lactuca, Antirrhinum, Pelargonium,Ranunculus, Senecio, Salpiglossis, Cucumis, Browallia, Glycine, Pisum,Phaseolus, and from the following monocot genera: Bromus, Asparagus,Hemerocallis, Panicum, Pennisetum, Lolium, Oryza, Avena, Hordeum,Secale, Triticum, Bambusa, Dendrocalamus, and Melocanna.

EXAMPLES

The present invention is further illustrated in the following Examples,in which parts and percentages are by weight and degrees are Celsius,unless otherwise stated. It should be understood that these Examples,while indicating preferred embodiments of the invention, are given byway of illustration only. From the above discussion and these Examples,one skilled in the art can ascertain the essential characteristics ofthis invention, and without departing from the spirit and scope thereof,can make various changes and modifications of the invention to adapt itto various usages and conditions. Thus, various modifications of theinvention in addition to those shown and described herein will beapparent to those skilled in the art from the foregoing description.Such modifications are also intended to fall within the scope of theappended claims.

Example 1 Composition of cDNA Libraries; Isolation and Sequencing ofcDNA Clones

cDNA libraries representing mRNAs from various cattail, corn, rice andsoybean tissues were prepared. The characteristics of the libraries aredescribed below. TABLE 2 cDNA Libraries from Cattail, Corn, Rice andSoybean Library Tissue Clone etr1c Cattail (Typha latifolia) rootetr1c.pk005.f8 p0075 Corn, root/leaf material from dark-grown 7p0075.cslaf22f day old Seedlings p0075.cslaf22rb p0128 Corn, pooledprimary and secondary p0128.cpicz81r immature ear rdi1c Rice (Oryzasativa, Nipponbare) developing rdi1c.pk001.a22 inflorescence at mitoticstage rth1c Rice leaf inoculated with Magnaporta grisea rth1c.pk009.k14fsdp3c Soybean developing pods 8-9 mm sdp3c.pk003.e22 ses4d Soybeanembryogenic suspension 4 days ses4d.pk0018.d10 after subculture sdp2cSoybean developing pods 6-7 mm sdp2c.pk008.m2 ssm Soybean shoot meristemssm.pk0072.e7 ssl Soybean seedling 5-10 day ssl.pk0021.h3 sgs4c Soybeanseeds 2 days after germination sgs4c.pk005.b10

cDNA libraries may be prepared by any one of many methods available. Forexample, the cDNAs may be introduced into plasmid vectors by firstpreparing the cDNA libraries in Uni-ZAP™ XR vectors according to themanufacturer's protocol (Stratagene Cloning Systems, La Jolla, Calif.).The Uni-ZAP™ XR libraries are converted into plasmid libraries accordingto the protocol provided by Stratagene. Upon conversion, cDNA insertswill be contained in the plasmid vector pBluescript. In addition, thecDNAs may be introduced directly into precut Bluescript II SK(+) vectors(Stratagene) using T4 DNA ligase (New England Biolabs), followed bytransfection into DH10B cells according to the manufacturer's protocol(GIBCO BRL Products). Once the cDNA inserts are in plasmid vectors,plasmid DNAs are prepared from randomly picked bacterial coloniescontaining recombinant pBluescript plasmids, or the insert cDNAsequences are amplified via polymerase chain reaction using primersspecific for vector sequences flanking the inserted cDNA sequences.Amplified insert DNAs or plasmid DNAs are sequenced in dye-primersequencing reactions to generate partial cDNA sequences (expressedsequence tags or “ESTs”; see Adams et al., (1991) Science252:1651-1656). The resulting ESTs are analyzed using a Perkin ElmerModel 377 fluorescent sequencer.

Example 2 Identification of cDNA Clones

cDNA clones encoding plastidic phosphoglucomutase proteins wereidentified by conducting BLAST (Basic Local Alignment Search Tool;Altschul et al. (1993) J. Mol. Biol. 215:403-410) searches forsimilarity to sequences contained in the BLAST “nr” database (comprisingall non-redundant GenBank CDS translations, sequences derived from the3-dimensional structure Brookhaven Protein Data Bank, the last majorrelease of the SWISS-PROT protein sequence database, EMBL, and DDBJdatabases). The cDNA sequences obtained in Example 1 were analyzed forsimilarity to all publicly available DNA sequences contained in the “nr”database using the BLASTN algorithm provided by the National Center forBiotechnology Information (NCBI). The DNA sequences were translated inall reading frames and compared for similarity to all publicly availableprotein sequences contained in the “nr” database using the BLASTXalgorithm (Gish and States (1993) Nat. Genet. 3:266-272) provided by theNCBI. For convenience, the P-value (probability) of observing a match ofa cDNA sequence to a sequence contained in the searched databases merelyby chance as calculated by BLAST are reported herein as “pLog” values,which represent the negative of the logarithm of the reported P-value.Accordingly, the greater the pLog value, the greater the likelihood thatthe cDNA sequence and the BLAST “hit” represent homologous proteins.

Example 3 Characterization of cDNA Clones Encoding PlastidicPhosphoglucomutase Proteins

The BLASTX search using the EST sequences from clones listed in Table 3revealed similarity of the polypeptides encoded by the cDNAs toplastidic phosphoglucomutase from Brassica napus (NCBI GeneralIdentifier No. 6272125) and Pisum sativum (NCBI General Identifier No.6272283 and NCBI General Identifier No. 10190529). Shown in Table 3 arethe BLAST results for individual ESTs (“EST”), the sequences of theentire cDNA inserts comprising the indicated cDNA clones (“FIS”),contigs assembled from two or more ESTs (“Contig”), contigs assembledfrom an FIS and one or more ESTs (“Contig*”), or sequences encoding theentire protein derived from an FIS, a contig, an EST and PCR, or an FISand PCR (“CGS”): TABLE 3 BLAST Results for Sequences EncodingPolypeptides Homologous to Brassica napus and Pisum sativum PlastidicPhosphoglucomutase Clone Status BLAST pLog Score etr1c.pk005.f8 (FIS)CGS >254.00 (GI No. 6272125; B. napus) Contig Composed of: CGS >254.00(GI No. 6272283; p0075.cslaf22f (EST) P. sativum) p0075.cslaf22rb (EST)p0128.cpicz81r (EST) rth1c.pk009.k14f (EST) EST    58.00 (GI No.6272283; P. sativum) sdp3c.pk003.e22 (EST CGS >254.00 (GI No. 6272283;and PCR Fragments) P. sativum) rdi1c.pk001.a22 (FIS) CGS   180.00 (GINo. 10190529; P. sativum)

The data in Table 4 represents a calculation of the percent identity ofthe amino acid sequences set forth in SEQ ID NOs:2, 4, 6, 8, and 10, andthe Brassica napus and Pisum sativum sequences. TABLE 4 Percent Identityof Amino Acid Sequences Deduced From the Nucleotide Sequences of cDNAClones Encoding Polypeptides Homologous to Brassica napus and Pisumsativum Plastidic Phosphoglucomutase SEQ ID NO. Percent Identity to 279% (GI No. 6272125; B. napus) 4 77% (GI No. 6272283; P. sativum) 6 80%(GI No. 6272283; P. sativum) 8 90% (GI No. 6272283; P. sativum) 10 76%(GI No. 10190529; P. sativum)

Sequence alignments and percent identity calculations were performedusing the Megalign program of the LASERGENE bioinformatics computingsuite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequenceswas performed using the Clustal method of alignment (Higgins and Sharp(1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10,GAP LENGTH PENALTY=10). Default parameters for pairwise alignments usingthe Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALSSAVED=5. Sequence alignments, BLAST scores and probabilities indicatethat the nucleic acid fragments comprising the instant cDNA clonesencode a substantial portion of a plastidic phosphoglucomutase.

Example 4 Expression of Chimeric Genes In Monocot Cells

A chimeric gene comprising a cDNA encoding the instant polypeptides insense orientation with respect to the maize 27 kD zein promoter that islocated 5′ to the cDNA fragment, and the 10 kD zein 3′ end that islocated 3′ to the cDNA fragment, can be constructed. The cDNA fragmentof this gene may be generated by polymerase chain reaction (PCR) of thecDNA clone using appropriate oligonucleotide primers. Cloning sites(NcoI or SmaI) can be incorporated into the oligonucleotides to provideproper orientation of the DNA fragment when inserted into the digestedvector pML103 as described below. Amplification is then performed in astandard PCR. The amplified DNA is then digested with restrictionenzymes NcoI and SmaI and fractionated on an agarose gel. Theappropriate band can be isolated from the gel and combined with a 4.9 kbNcoI-SmaI fragment of the plasmid pML103. Plasmid pML103 has beendeposited under the terms of the Budapest Treaty at ATCC (American TypeCulture Collection, 10801 University Blvd., Manassas, Va. 20110-2209),and bears accession number ATCC 97366. The DNA segment from pML103contains a 1.05 kb SalI-NcoI promoter fragment of the maize 27 kD zeingene and a 0.96 kb SmaI-SalI fragment from the 3′ end of the maize 10 kDzein gene in the vector pGem9Zf(+) (Promega). Vector and insert DNA canbe ligated at 15° C. overnight, essentially as described (Maniatis). Theligated DNA may then be used to transform E. coli XL1-Blue (EpicurianColi XL-1 Blue™; Stratagene). Bacterial transformants can be screened byrestriction enzyme digestion of plasmid DNA and limited nucleotidesequence analysis using the dideoxy chain termination method (Sequenase□DNA Sequencing Kit; U.S. Biochemical). The resulting plasmid constructwould comprise a chimeric gene encoding, in the 5′ to 3′ direction, themaize 27 kD zein promoter, a cDNA fragment encoding the instantpolypeptides, and the 10 kD zein 3′ region.

The chimeric gene described above can then be introduced into corn cellsby the following procedure. Immature corn embryos can be dissected fromdeveloping caryopses derived from crosses of the inbred corn lines H99and LH132. The embryos are isolated 10 to 11 days after pollination whenthey are 1.0 to 1.5 mm long. The embryos are then placed with theaxis-side facing down and in contact with agarose-solidified N6 medium(Chu et al. (1975) Sci. Sin. Peking 18:659-668). The embryos are kept inthe dark at 27° C. Friable embryogenic callus consisting ofundifferentiated masses of cells with somatic proembryoids and embryoidsborne on suspensor structures proliferates from the scutellum of theseimmature embryos. The embryogenic callus isolated from the primaryexplant can be cultured on N6 medium and sub-cultured on this mediumevery 2 to 3 weeks.

The plasmid, p35S/Ac (obtained from Dr. Peter Eckes, Hoechst Ag,Frankfurt, Germany) may be used in transformation experiments in orderto provide for a selectable marker. This plasmid contains the Pat gene(see European Patent Publication 0 242 236) which encodesphosphinothricin acetyl transferase (PAT). The enzyme PAT confersresistance to herbicidal glutamine synthetase inhibitors such asphosphinothricin. The pat gene in p35S/Ac is under the control of the35S promoter from Cauliflower Mosaic Virus (Odell et al. (1985) Nature313:810-812) and the 3′ region of the nopaline synthase gene from theT-DNA of the Ti plasmid of Agrobacterium tumefaciens.

The particle bombardment method (Klein et al. (1987) Nature 327:70-73)may be used to transfer genes to the callus culture cells. According tothis method, gold particles (1 μm in diameter) are coated with DNA usingthe following technique. Ten μg of plasmid DNAs are added to 50 μL of asuspension of gold particles (60 mg per mL). Calcium chloride (50 μL ofa 2.5 M solution) and spermidine free base (20 μL of a 1.0 M solution)are added to the particles. The suspension is vortexed during theaddition of these solutions. After 10 minutes, the tubes are brieflycentrifuged (5 sec at 15,000 rpm) and the supernatant removed. Theparticles are resuspended in 200 μL of absolute ethanol, centrifugedagain and the supernatant removed. The ethanol rinse is performed againand the particles resuspended in a final volume of 30 μL of ethanol. Analiquot (5 μL) of the DNA-coated gold particles can be placed in thecenter of a Kapton™ flying disc (Bio-Rad Labs). The particles are thenaccelerated into the corn tissue with a Biolistic™ PDS-1000/He (Bio-RadInstruments, Hercules Calif.), using a helium pressure of 1000 psi, agap distance of 0.5 cm and a flying distance of 1.0 cm.

For bombardment, the embryogenic tissue is placed on filter paper overagarose-solidified N6 medium. The tissue is arranged as a thin lawn andcovered a circular area of about 5 cm in diameter. The petri dishcontaining the tissue can be placed in the chamber of the PDS-1000/Heapproximately 8 cm from the stopping screen. The air in the chamber isthen evacuated to a vacuum of 28 inches of Hg. The macrocarrier isaccelerated with a helium shock wave using a rupture membrane thatbursts when the He pressure in the shock tube reaches 1000 psi.

Seven days after bombardment the tissue can be transferred to N6 mediumthat contains glufosinate (2 mg per liter) and lacks casein or proline.The tissue continues to grow slowly on this medium. After an additional2 weeks the tissue can be transferred to fresh N6 medium containingglufosinate. After 6 weeks, areas of about 1 cm in diameter of activelygrowing callus can be identified on some of the plates containing theglufosinate-supplemented medium. These calli may continue to grow whensub-cultured on the selective medium.

Plants can be regenerated from the transgenic callus by firsttransferring clusters of tissue to N6 medium supplemented with 0.2 mgper liter of 2,4-D. After two weeks the tissue can be transferred toregeneration medium (Fromm et al. (1990) Bio/Technology 8:833-839).

Example 5 Expression of Chimeric Genes In Dicot Cells

A seed-specific construct composed of the promoter and transcriptionterminator from the gene encoding the □ subunit of the seed storageprotein phaseolin from the bean Phaseolus vulgaris (Doyle et al. (1986)J. Biol. Chem. 261:9228-9238) can be used for expression of the instantpolypeptides in transformed soybean. The phaseolin construct includesabout 500 nucleotides upstream (5′) from the translation initiationcodon and about 1650 nucleotides downstream (3′) from the translationstop codon of phaseolin. Between the 5′ and 3′ regions are the uniquerestriction endonuclease sites Nco I (which includes the ATG translationinitiation codon), Sma I, Kpn I and Xba I. The entire construct isflanked by Hind III sites.

The cDNA fragment of this gene may be generated by polymerase chainreaction (PCR) of the cDNA clone using appropriate oligonucleotideprimers. Cloning sites can be incorporated into the oligonucleotides toprovide proper orientation of the DNA fragment when inserted into theexpression vector. Amplification is then performed as described above,and the isolated fragment is inserted into a pUC18 vector carrying theseed construct.

Soybean embryos may then be transformed with the expression vectorcomprising sequences encoding the instant polypeptides. To inducesomatic embryos, cotyledons, 3-5 mm in length dissected from surfacesterilized, immature seeds of the soybean cultivar A2872, can becultured in the light or dark at 26° C. on an appropriate agar mediumfor 6-10 weeks. Somatic embryos which produce secondary embryos are thenexcised and placed into a suitable liquid medium. After repeatedselection for clusters of somatic embryos which multiplied as early,globular staged embryos, the suspensions are maintained as describedbelow.

Soybean embryogenic suspension cultures can be maintained in 35 mL ofliquid media on a rotary shaker, 150 rpm, at 26° C. with florescentlights on a 16:8 hour day/night schedule. Cultures are subcultured everytwo weeks by inoculating approximately 35 mg of tissue into 35 mL ofliquid medium.

Soybean embryogenic suspension cultures may then be transformed by themethod of particle gun bombardment (Klein et al. (1987) Nature (London)327:70-73, U.S. Pat. No. 4,945,050). A DuPont Biolistic™ PDS1000/HEinstrument (helium retrofit) can be used for these transformations.

A selectable marker gene which can be used to facilitate soybeantransformation is a chimeric gene composed of the 35S promoter fromCauliflower Mosaic Virus (Odell et al. (1985) Nature 313:810-812), thehygromycin phosphotransferase gene from plasmid pJR225 (from E. coli;Gritz et al.(1983) Gene 25:179-188) and the 3′ region of the nopalinesynthase gene from the T-DNA of the Ti plasmid of Agrobacteriumtumefaciens. The seed construct comprising the phaseolin 5′ region, thefragment encoding the instant polypeptides and the phaseolin 3′ regioncan be isolated as a restriction fragment. This fragment can then beinserted into a unique restriction site of the vector carrying themarker gene.

To 50 μL of a 60 mg/mL 1 μm gold particle suspension is added (inorder): 5 μL DNA (1 μg/μL), 20 μL spermidine (0.1 M), and 50 μL CaCl₂(2.5 M). The particle preparation is then agitated for three minutes,spun in a microfuge for 10 seconds and the supernatant removed. TheDNA-coated particles are then washed once in 400 μL 70% ethanol andresuspended in 40 μL of anhydrous ethanol. The DNA/particle suspensioncan be sonicated three times for one second each. Five μL of theDNA-coated gold particles are then loaded on each macro carrier disk.

Approximately 300-400 mg of a two-week-old suspension culture is placedin an empty 60×15 mm petri dish and the residual liquid removed from thetissue with a pipette. For each transformation experiment, approximately5-10 plates of tissue are normally bombarded. Membrane rupture pressureis set at 1100 psi and the chamber is evacuated to a vacuum of 28 inchesof mercury. The tissue is placed approximately 3.5 inches away from theretaining screen and bombarded three times. Following bombardment, thetissue can be divided in half and placed back into liquid and culturedas described above.

Five to seven days post bombardment, the liquid media may be exchangedwith fresh media, and eleven to twelve days post bombardment with freshmedia containing 50 mg/mL hygromycin. This selective media can berefreshed weekly. Seven to eight weeks post bombardment, green,transformed tissue may be observed growing from untransformed, necroticembryogenic clusters. Isolated green tissue is removed and inoculatedinto individual flasks to generate new, clonally propagated, transformedembryogenic suspension cultures. Each new line may be treated as anindependent transformation event. These suspensions can then besubcultured and maintained as clusters of immature embryos orregenerated into whole plants by maturation and germination ofindividual somatic embryos.

Example 6 Expression of Chimeric Genes In Microbial Cells

The cDNAs encoding the instant polypeptides can be inserted into the T7E. coli expression vector pBT430. This vector is a derivative of pET-3a(Rosenberg et al. (1987) Gene 56:125-135) which employs thebacteriophage T7 RNA polymerase/T7 promoter system. Plasmid pBT430 wasconstructed by first destroying the EcoR I and Hind III sites in pET-3aat their original positions. An oligonucleotide adaptor containing EcoRI and Hind III sites was inserted at the BamH I site of pET-3a. Thiscreated pET-3aM with additional unique cloning sites for insertion ofgenes into the expression vector. Then, the Nde I site at the positionof translation initiation was converted to an Nco I site usingoligonucleotide-directed mutagenesis. The DNA sequence of pET-3aM inthis region, 5′-CATATGG, was converted to 5′-CCCATGG in pBT430.

Plasmid DNA containing a cDNA may be appropriately digested to release anucleic acid fragment encoding the protein. This fragment may then bepurified on a 1% NuSieve GTG™ low melting agarose gel (FMC). Buffer andagarose contain 10 μg/mL ethidium bromide for visualization of the DNAfragment. The fragment can then be purified from the agarose gel bydigestion with GELase™ (Epicentre Technologies) according to themanufacturer's instructions, ethanol precipitated, dried and resuspendedin 20 μL of water. Appropriate oligonucleotide adapters may be ligatedto the fragment using T4 DNA ligase (New England Biolabs, Beverly,Mass.). The fragment containing the ligated adapters can be purifiedfrom the excess adapters using low melting agarose as described above.The vector pBT430 is digested, dephosphorylated with alkalinephosphatase (NEB) and deproteinized with phenol/chloroform as describedabove. The prepared vector pBT430 and fragment can then be ligated at16° C. for 15 hours followed by transformation into DH5 electrocompetentcells (GIBCO BRL). Transformants can be selected on agar platescontaining LB media and 100 μg/mL ampicillin. Transformants containingthe gene encoding the instant polypeptides are then screened for thecorrect orientation with respect to the T7 promoter by restrictionenzyme analysis.

For high level expression, a plasmid clone with the cDNA insert in thecorrect orientation relative to the T7 promoter can be transformed intoE. coli strain BL21 (DE3) (Studier et al. (1986) J. Mol. Biol.189:113-130). Cultures are grown in LB medium containing ampicillin (100mg/L) at 25° C. At an optical density at 600 nm of approximately 1, IPTG(isopropylthio-β-galactoside, the inducer) can be added to a finalconcentration of 0.4 mM and incubation can be continued for 3 h at 25°C. Cells are then harvested by centrifugation and re-suspended in 50 μLof 50 mM Tris-HCl at pH 8.0 containing 0.1 mM DTT and 0.2 mM phenylmethylsulfonyl fluoride. A small amount of 1 mm glass beads can be addedand the mixture sonicated 3 times for about 5 seconds each time with amicroprobe sonicator. The mixture is centrifuged and the proteinconcentration of the supernatant determined. One μg of protein from thesoluble fraction of the culture can be separated by SDS-polyacrylamidegel electrophoresis. Gels can be observed for protein bands migrating atthe expected molecular weight.

Example 7 Transformation of Somatic Soybean Embryo Cultures

Generic Stable Soybean Transformation Protocol:

Soybean embryogenic suspension cultures are maintained in 35 ml liquidmedia (SB55 or SBP6) on a rotary shaker, 150 rpm, at 28° C. with mixedfluorescent and incandescent lights on a 16:8 h day/night schedule.Cultures are subcultured every four weeks by inoculating approximately35 mg of tissue into 35 ml of liquid medium. TABLE 5 Stock Solutions(g/L): MS Sulfate 100X Stock MgSO₄ 7H₂O 37.0 MnSO₄ H₂O 1.69 ZnSO₄ 7H₂O0.86 CuSO₄ 5H₂O 0.0025 MS Halides 100X Stock CaCl₂ 2H₂O 44.0 Kl 0.083CoCl₂ 6H₂0 0.00125 KH₂PO₄ 17.0 H₃BO₃ 0.62 Na₂MoO₄ 2H₂O 0.025 MS FeEDTA100X Stock Na₂EDTA 3.724 FeSO₄ 7H₂O 2.784 B5 Vitamin Stock 10 gm-inositol 100 mg nicotinic acid 100 mg pyridoxine HCl 1 g thiamine SB55(per Liter, pH 5.7) 10 ml each MS stocks 1 ml B5 Vitamin stock 0.8 gNH₄NO₃ 3.033 g KNO₃ 1 ml 2,4-D (10 mg/mL stock) 60 g sucrose 0.667 gasparagine SBP6 same as SB55 except 0.5 ml 2,4-D SB103 (per Liter, pH5.7) 1X MS Salts 6% maltose 750 mg MgCl₂ 0.2% Gelrite SB71-1 (per Liter,pH 5.7) 1X B5 salts 1 ml B5 vitamin stock 3% sucrose 750 mg MgCl₂ 0.2%Gelrite

Soybean embryogenic suspension cultures are transformed with plasmid DNAby the method of particle gun bombardment (Klein et al (1987) Nature327:70). A DuPont Biolistic™ PDS1000/HE instrument (helium retrofit) isused for these transformations.

To 50 ml of a 60 mg/ml 1 μm gold particle suspension is added (inorder); 5 μl DNA(1 μg/μl), 20 μl spermidine (0.1 M), and 50 μl CaCl₂(2.5 M). The particle preparation is agitated for 3 min, spun in amicrofuge for 10 sec and the supernatant removed. The DNA-coatedparticles are then washed once in 400 μl 70% ethanol and re suspended in40 μl of anhydrous ethanol. The DNA/particle suspension is sonicatedthree times for 1 sec each. Five μl of the DNA-coated gold particles arethen loaded on each macro carrier disk. For selection, a plasmidconferring resistance to hygromycin phosphotransferase (HPT) may beco-bombarded with the silencing construct of interest.

Approximately 300-400 mg of a four week old suspension culture is placedin an empty 60×15 mm petri dish and the residual liquid removed from thetissue with a pipette. For each transformation experiment, approximately5-10 plates of tissue are normally bombarded. Membrane rupture pressureis set at 1000 psi and the chamber is evacuated to a vacuum of 28 inchesof mercury. The tissue is placed approximately 3.5 inches away from theretaining screen and bombarded three times. Following bombardment, thetissue is placed back into liquid and cultured as described above.

Eleven days post bombardment, the liquid media is exchanged with freshSB55 containing 50 mg/ml hygromycin. The selective media is refreshedweekly. Seven weeks post bombardment, green, transformed tissue isobserved growing from untransformed, necrotic embryogenic clusters.Isolated green tissue is removed and inoculated into individual flasksto generate new, clonally propagated, transformed embryogenic suspensioncultures. Thus each new line is treated as an independent transformationevent. These suspensions can then be maintained as suspensions ofembryos maintained in an immature developmental stage or regeneratedinto whole plants by maturation and germination of individual somaticembryos.

Independent lines of transformed embryogenic clusters are removed fromliquid culture and placed on a solid agar media (SB103) containing nohormones or antibiotics. Embryos are cultured for four weeks at 26° C.with mixed fluorescent and incandescent lights on a 16:8 h day/nightschedule. During this period, individual embryos are removed from theclusters and screened for alterations in gene expression.

It should be noted that any detectable phenotype, resulting from thecosuppression of a target gene, can be screened at this stage. Thiswould include, but not be limited to, alterations in protein content,carbohydrate content, growth rate, viability, or the ability to developnormally into a soybean plant.

Example 8 Plasmid DNAs for “Complementary Region” Co-Suppression

The plasmids used in these experiments were made using standard cloningmethods well known to those skilled in the art (Sambrook et al (1989)Molecular Cloning, CSHL Press, New York). A starting plasmid pKS18HH(U.S. Pat. No. 5,846,784 the contents of which are hereby incorporatedby reference) contains a hygromycin B phosphotransferase (HPT) obtainedfrom E. coli strain W677 under the control of a T7 promoter and the 35Scauliflower mosaic virus promoter. Plasmid pKS18HH thus contains the T7promoter/HPT/T7 terminator cassette for expression of the HPT enzyme incertain strains of E. coli, such as NovaBlue(DE3) [from Novagen], thatare lysogenic for lambda DE3 (which carries the T7 RNA Polymerase geneunder IacV5 control). Plasmid pKS18HH also contains the 35S/HPT/NOScassette for constitutive expression of the HPT enzyme in plants, suchas soybean. These two expression systems allow selection for growth inthe presence of hygromycin to be used as a means of identifying cellsthat contain the plasmid in both bacterial and plant systems. pKS18HHalso contains three unique restriction endonuclease sites suitable forthe cloning other chimeric genes into this vector. Plasmid ZBL100 (PCTApplication No. WO 00/11176 published on Mar. 2, 2000) is a derivativeof pKS18HH with a reduced NOS 3′ terminator. Plasmid pKS67 is a ZBL100derivative with the insertion of a beta-conglycinin promoter, in frontof a NotI cloning site, followed by a phaseolin 3′ terminator (describedin PCT Application No. WO 94/11516, published on May 26, 1994).

The 2.5 kb plasmid pKS17 contains pSP72 (obtained from PromegaBiosystems) and the T7 promoter/HPT/T7 3′ terminator region, and is theoriginal vector into which the 3.2 kb BamHI-SalI fragment containing the35S/HPT/NOS cassette was cloned to form pKS18HH. The plasmid pKS102 is apKS17 derivative that is digested with XhoI and SalI, treated withmung-bean nuclease to generate blunt ends, and ligated to insert thefollowing linker:

-   GGCGCGCCMGCTTGGATCCGTCGACGGCGCGCC SEQ ID NO:18

The plasmid pKS83 has the 2.3 kb BamHI fragment of ML70 containing theKti3 promoter/NotI/Kti3 3′ terminator region (described in PCTApplication No. WO 94/11516, published on May 26, 1994) ligated into theBamHI site of pKS17.

Example 9 Suppression By ELVISLIVES Complementary Region

Constructs have now been made which have “synthetic complementaryregions” (SCR). In this example the target sequence is placed betweencomplementary sequences that are not known to be part of anybiologically derived gene or genome (i.e. sequences that are “synthetic”or conjured up from the mind of the inventor). The target DNA wouldtherefore be in the sense or antisense orientation and the complementaryRNA would be unrelated to any known nucleic acid sequence. It ispossible to design a standard “suppression vector” into which pieces ofany target gene for suppression could be dropped. The plasmids pKS106,pKS124, and pKS133 (SEQ ID NO:17) exemplify this. One skilled in the artwill appreciate that all of the plasmid vectors contain antibioticselection genes such as, but not limited to, hygromycinphosphotransferase with promoters such as the T7 inducible promoter.

pKS106 uses the beta-conglycinin promoter while the pKS124 and pKS133plasmids use the Kti promoter, both of these promoters exhibit strongtissue specific expression in the seeds of soybean. pKS106 uses a 3′termination region from the phaseolin gene, and pKS124 and pKS133 use aKti 3′ termination region. pKS106 and pKS124 have single copies of the36 nucleotide EagI-ELVISLIVES sequence surrounding a NotI site (theamino acids given in parentheses are back-translated from thecomplementary strand): SEQ ID NO:19 EagI E L V I S L I V E S NotI CGGCCGGAG CTG GTC ATC TCG CTC ATC GTC GAG TCG GCGGCCGC (S) (E) (V) (I) (L) (S)(I) (V) (L) (E) EagI CGA CTC GAC GAT GAG CGA GAT GAC CAG CTC CGGCCG

pKS133 has 2X copies of ELVISLIVES surrounding the NotI site: SEQ IDNO:20 EagI E L V I S L I V E S EagI E L V I Scggccggagctggtcatctcgctcatcgtcgagtcg gcggccg gagctggtcatctcg L I V E SNotI (S)(E (V)(I)(L)(S)(I)(V)(L)(E) EagI ctcatcgtcgagtcg gcggccgccgactcgacgatgagcgagatgaccagctc cggccgc (S)(E)(V)(I)(L)(S)(I)(V)(L)(E)EagI cgactcgacgatgagcgagatgaccagctc cggccg

The idea is that the single EL linker (SCR) can be duplicated toincrease stem lengths in increments of approximately 40 nucleotides. Aseries of vectors will cover the SCR lengths between 40 bp and the 300bp. Various target gene lengths are also under evaluation. It isbelieved that certain combinations of target lengths and complementaryregion lengths will give optimum suppression of the target, althoughpreliminary results would indicate that the suppression phenomenon workswell over a wide range of sizes and sequences. It is also believed thatthe lengths and ratios providing optimum suppression may vary somewhatgiven different target sequences and/or complementary regions.

The plasmid pKS106 is made by putting the EagI fragment of ELVISLIVES(SEQ ID NO:19) into the NotI site of pKS67. The ELVISLIVES fragment ismade by PCR using two primers and no other DNA: SEQ ID NO:21 5′-GAATTCCGGCCGGAGCTGGTCATCTCGCTCATCGTCGAGTCGGCGGCCGCCGACTCGACGATGAGCGAGATGACCAGCTCCGGCCGGAATTC-3′ SEQ ID NO:225′-GAATTCCGGCCGGAG-3′

The product of the PCR reaction is digested with EagI (5′-CGGCCG-3′) andthen ligated into NotI digested pKS67. The term “ELVISLIVES” and “EL”are used interchangeably herein.

Additional plasmids can be used to test this example. For example,pKS121 contains the Kti3 promoter/NotI/Kti3 3′ terminator fragmentanalogous to pKS83 inserted into the BamHI-SalI digested pKS102. TheEagI digested ELVISLIVES cloning site made from SEQ ID NOs:14 and 15 isinserted into the NotI site of pKS121 to form pKS124. The EagI digestedEL PCR product can be ligated into NotI digested pKS124 to form the 2XELplasmid, pKS133 (SEQ ID NO:17), containing two copies of ELVISLIVES. Anadditional 2XEL vector, pKS151, is similar to pKS133 except for theaddition of a second hygromycin phosphotransferase gene with a 35S-CaMVpromoter. Any synthetic sequence, or naturally occurring sequence, canbe used in an analogous manner. The addition of a 574 base pair NotIfragment (SEQ ID NO:14) into a NotI-digested pKS133 produces pTC103. The574 base pair Not I fragment (SEQ ID NO:14) contains a 541 base pairregion (SEQ ID NO:15) of the soybean plastid phosphoglucomutase codingregion (SEQ ID NO:8).

Example 10 Down Regulation of Plastidic Phosphoglucomutase In Soybean

Soybean was transformed with the plasmid DNA, pTC103, and transgeniclines were selected. Transgenic lines were screened for down regulationof plastidic phosphoglucomutase in soybean. The screening assay involvediodine staining for the presence or absence of starch in immature seeds(mid-pod stage). The method involved harvesting half of the seed, andputting that seed on dry ice and storing at −80 C. The other half of theseed was placed in 100% ethanol overnight, and subsequently stained withwater:lugoI (4:1) solution for 10 to 30 minutes at room temperature.LugoI is an iodine/potassium iodide solution, commercially availablefrom Sigma.

Four out of nineteen events showed a clear reduction in iodine stainingindicating a reduction in starch content. This may reflect a 21%cosuppression success with the hairpin construct. Three additionalevents showed potential, reduction in iodine staining, although thedifferences in staining were subtle. The segregation patterns of events100-2-1 and 108-3-1 are consistent with a theoretical segregation of adominant co-suppression (1:3). TABLE 6 Summary of Iodine Screen Sum +Events 4 − Events 12 ? Events 3 Total Events Analyzed 19 Events with no2 plants/sterile/dwarf Total Events 27

TABLE 7 Seed segregation information of potential positive pPGM events.D = dark blue stain, L = light blue or no stain, D/L in between dark andlight stain Event Plant D:L seed ratio Note 100-2-1 1 1:5 clear positive100-2-1 2 3:2 clear positive 100-2-1 3 1:5 clear positive 108-3-1 1 0:6clear positive 108-3-1 2 2:4 clear positive 108-3-1 3 1:5 clear positive105-2-3 1 4:0 negative 105-2-3 2 1:5 clear positive 105-1-6 1 4:0negative 105-1-6 3 2:2 clear positive 105-1-1 1 4:2 D/L 105-1-1 2 0:6D/L 105-1-1 3 6:0 D/L 101-2-6 1 6:0 D/L 101-2-6 3 2:3 D/L 102-3-3 1 2:3D/L 102-3-3 2 3:0 D/L

Example 11 Silencing of Plastidic Phosphoglucomutase (pPGM) Results In aStable Reduction of Transient Starch Accumulation In Developing SoybeanSeeds

Transgenic soybean events were produced as described in Example 10.Developing soybean seeds were harvested at approximately mid-maturity(20 to 30 days after flowering (DAF)) and starch content was quantifiedas described in Brown and Huber, Physiologia Plantarum 72:518-524(1988). T1 seeds from three transgenic events showed about an 80%reduction in starch content as compared to wild-type seeds (Table 8).The starch data correlated with the iodine staining described in Example10, i.e., seeds that do not stain blue have a significant reduction instarch content while blue-staining seeds have starch contents similar towild-type TABLE 8 Starch Content of T1 Seeds (ApproximatelyMid-maturity) Segregating for Co-suppression of pPGM. B = Seeds StainingBlue. W = Seeds Not Staining. Blue Staining Indicates Presence ofStarch. Iodine Mg starch/g seed % of wild- Event score mean st. dev.type WT (Jack) B 22.83 5.69 100 108-3-1 W 5.20 2.24 20 108-3-1 B 25.92 —100 105-1-8 nd nd nd nd 100-2-1 W 5.27 1.66 22 100-2-1 B 24.27 5.40 100105-1-6 W 2.69 3.81 14 105-1-6 B 18.87 6.76 100nd = not determined

The soluble carbohydrate composition of developing transgenic seeds wasmeasured by high performance anion exchange chromatography/pulsedamperometric detection (HPAE/PAD). Individual seeds from transgeniclines were harvested at mid-maturity (20 to 30 DAF) for detection ofcarbohydrate composition. The seeds were frozen in liquid nitrogen,ground with a mortar and pestle, and transferred to 15 mlmicrocentrifuge tubes. Ethanol (80%) was added to the tubes and thesamples were heated to 70° C. for 15 minutes. Samples were centrifugedat 4000 rpm for 15 minutes at 4° C. and the supernatant collected. Thepellet was re-extracted two additional times with 80% ethanol at 70° C.The supernatants were combined, dried down in a speedvac, and the pelletre-suspended in water. Furthermore, the extracts were filtered through a0.2 μm Nylon-66 filter (Rainin, Emeryville, Calif.) and analyzed byHPAE/PAD using a DX500 anion exchange analyzer (Dionex, Sunnyvale,Calif.) equipped with a 250×4 mm CarboPac PA1 anion exchange column anda 25×4 mm CarboPac PA guard column. Soluble carbohydrates were separatedwith a 30 minute isocratic run of 0.5 mM NaAc in 150 mM NaOH at a flowrate of 1.0 mL/min. A dilution series of glucose, fructose, sucrose,raffinose, stachyose and verbascose were used as external standards.

Soluble carbohydrate analysis on 6 seeds per event segregating foriodine staining (starch presence) indicated no major change inconcentration of sucrose and total soluble carbohydrates atapproximately mid-maturity (Table 9). No raffinose familyoligosaccharides (RFOs) were observed at this stage of development;hence, no sucrose to RFO ratio could be determined. TABLE 9 Sucrose andTotal Soluble Sugar Content (mg/g seed) of Segregating T1 SeedsHarvested at Mid-maturity. D = Dark Blue Stain, L = Light Blue or NoStain Total Soluble Plant Seed Sucrose Sugars Event No. Score mean std.mean std. 108-3-1 1 L 22.8 3.1 26.5 3.8 108-3-1 3 D 13.1 — 17.2 —108-3-1 3 L 10.4 5.9 14.7 5.4 105-1-8 nd* nd nd nd nd 100-2-1 2 D 16.04.7 21.0 6.0 100-2-1 2 L 18.6 4.7 24.3 5.6 105-1-6 1 D 31.5 12.5 36.43.8 105-1-6 3 D 23.1 2.6 27.3 2.6 105-1-6 3 L 18.2 5.2 23.4 5.4nd* = not determined

T1 seeds from event 108-3-1 were planted in a growth chamber and T2seeds were harvested at mid-maturity and screened for starch presenceusing the iodine screen described in Example 10. Starch and solublecarbohydrate content of T2 seeds were determined as described above.

T2 seeds in which the pPGM gene is silenced (referred to as PGM-KO)showed an 80% decrease in starch content (Table 10). Null-segregating T2seeds were also identified which had wild-type starch levels (referredto as PGM-WT). No major differences in soluble carbohydrateconcentrations between pPGM-silenced T2 seeds (PGM-KO) and wild-typeseeds (Jack or PGM-WT) were observed at this stage of development. Thisdata is similar to data obtained from T1 seeds (Table 8 and Table 9) andsuggest that the event is inherited in a stable manner. TABLE 10 Starch,Sucrose and Total Soluble Carbohydrate Content of T2 Seeds (GrowthChamber Grown) from pPGM-Silenced Seeds Harvested at Mid-maturity. B =Seeds Staining Blue. W = Seeds Not Staining. Blue Staining IndicatesPresence of Starch. mg mg mg Total Starch/g Iodine Sucrose/ CHOs/g Seed% of Name Event Score g Seed Seed (mean) WT Jack Control B 15.9 19.822.83 100 PGM-KO 108-3-1 W 14.8 21.3 3.7 22 PGM-WT 108-3-1 B 16.6 19.716.89 100

Starch quantitation of developing soybean seeds harvested at 20, 30, 40and 50 DAF indicated that throughout seed development, the starchaccumulation of a pPGM-silenced soybean was reduced by 85% as comparedto its null segregant (FIG. 2).

Example 12

Silencing of Plastidic Phosphoglucomutase Decreases Total CarbohydrateContent and Alters the Sucrose To Raffinose Family Oligosaccharide RatioIn Mature Seeds

Transgenic T2 soybean seeds were harvested at mid-maturity and screenedfor reduced starch content using the iodine screen described in Example10. In total, three thousand seeds (field and growth chamber grown) from436 plants representing 21 different events were screened. A secondaryscreen using 20 seeds per plant was conducted to identify potentialhomozygotes. Five events (108-3-1, 105-1-8, 100-2-1, 105-1-7 and100-3-2) showed a decreased or no iodine staining.

Carbohydrate analysis (determined as described in Example 11) of matureT2 seeds from plants grown in a growth chamber (GC) revealed a decreasein total soluble carbohydrates of approximately 11% with sucrose beingthe major sugar affected (38% decrease) as compared to their nullsegregant (FIG. 3). Carbohydrate analysis of field grown events revealeda decrease in total soluble carbohydrates of approximately 14 to 25%together with a 30 to 39% decrease in sucrose. In both the growthchamber and field grown plants, mature seeds from the pPGM-silencedevents (PGM-KO) were characterized with a distinctive change in sucroseto RFO ratio. Under these conditions the sucrose to RFO ratio ofwild-type seeds averaged around 1.3 to 1.7 while the sucrose to RFOratio of pPGM cosuppressed seeds averaged around 0.7 to 0.9.

Seeds from a selected number of events were grown in a growth chamber toproduce T3 seeds. Carbohydrate analysis of T3 seeds from pPGM-silencedevents revealed a decrease in total soluble carbohydrates ofapproximately 24 to 35% as compared to their wild-type. Sucrose contentdecreased by 35 to 48% whereas RFO decreased by approximately 14% (FIG.4).

The carbohydrate profile of these T3 seeds is thus very similar to R2seeds and indicates (as was seen with the starch content) that the pPGMtrait is inherited in a stable manner. The sucrose to RFO ratio of pPGMco-suppressed R3 seeds (ratio of 1.2 to 1.5) was as compared to the nullsegregant (ratio of 1.6 to 2.0). Although the sucrose to RFO ratio in T3seeds is somewhat higher as compared to T2 seeds, the decrease in thesucrose to RFO ratio between pPGM co-suppressed seeds and wild-typeseeds averages around 0.5.

Example 13 Silencing of Plastidic Phosphoglucomutase (pPGM) Results Inan Increased Accumulation of Oil and/or Protein In Mature Seeds

Total oil and protein content of mature T2 seeds from event 108-3-1-1showing a pPGM-silenced phenotype was determined and compared to the oiland protein content of a pPGM null segregant (wild-type phenotype) fromthe same event (Table 11). Percent oil and percent protein changes wereexpressed on a seed dry weight basis. Seed composition of wild-type92B91 was performed as a control reference. Protein and oil weremeasured by Woodson-Tenant Labs (Des Moines, Iowa), using standard AOACmethods; combustion method for protein (AOAC Official Method 990.03;2000 AOAC International), and ether extraction method for oil (AOACOfficial Method 920.39; 2000 AOAC International).

Field grown pPGM-silenced seeds showed an increased oil content of up to2% on a seed dry wt basis and a slightly increased protein content (1%on a seed dry wt basis) as compared to seeds from the null segregant.Total oil content of growth chamber grown pPGM co-suppressed seedsincreased by 4% on a seed dry wt basis. This high increase in oilcontent was accompanied with a decreased protein content (Table 11). Nomajor difference was observed between the seed composition of PGM-WT andthe wild-type cultivar 92B91. TABLE 11 Seed Composition of T2 seeds froma pPGM-Silenced Line (PGM-KO) and a Null Segregant (PGM-WT) for Event108-3-1-1 Growth % % % Oil & Con- Pheno- Pro- % Oil Protein Protein IDdition type % Oil tein Increase Increase Increase 2097-7 Growth PGM-23.39 37.08 4.19 −3.04 1.15 Cham- KO ber 2097-7 Field PGM- 21.22 41.252.20 +1.12 3.32 KO 2097-1 Field PGM- 19.20 40.12 — — — WT 92B91 Fieldwild- 20.36 40.40 — — — type

T2 seeds from event 108-3-1-1 were planted in a growth chamber toproduce T3 seeds. This T3 generation of mature seeds from pPGMco-suppressed seeds showed the greatest increase in protein contentrather than oil content when compared to their null segregant (Table 12;percent oil and percent protein changes were calculated on a seed dryweight basis). Interestingly, the sum of both increase in oil andprotein content was similar for T3 seeds from both plants, ranging from1.76 to 1.83%, on a seed dry wt basis. TABLE 12 Seed Composition of T3Seeds from Two pPGM-Silenced Plants (PGM-KO) and a Null Segregant(PGM-WT) % % % Oil & Pheno- Pro- % Oil Protein Protein Event ID type %Oil tein Increase Increase Increase 108-3-1-1 JS1- PGM-KO 22.03 40.09−0.61   2.37 1.76 261 108-3-1-1 JS2- PGM-KO 22.99 39.21 0.35 1.49 1.83265 108-3-1-1 JS3- PGM-WT 22.64 37.72 — — — 2642

T3 seeds from several other events having cv. Jack as their geneticbackground showed similar trends as observed with the event 108-3-1-1,which has cv. 92B91 as its genetic background. The increase in the sumof oil and protein content ranged from 0.98 to 3.14% as expressed on aseed dry wt basis (Table 13). TABLE 13 Seed Composition of T3 Seeds frompPGM-Silenced (PGM-KO) and PGM Wild-Type (PGM-WT) Events in a cv. JackBackground % Oil & Pheno- % % Oil % Protein Protein Event type % OilProtein Increase Increase Increase 101-2-6-3 PGM-WT 22.36 38.48 — — —105-1-8-2 PGM-KO 21.29 40.53 −1.07 2.05 0.98 100-2-1-1 PGM-KO 23.9240.06 1.56 1.58 3.14 100-2-1-1 PGM-KO 21.79 40.69 −0.57 2.21 1.64

Homozygous pPGM-silenced (PGM-KO) and pPGM-wild-type (PGM-WT) seeds,originating from crosses between pPGM knockout event and elitegermplasm, were grown in the field in 2003 and in 2004. The seedcompositions were determined and are shown in Table 14. The percent oil,percent protein and percent combined oil and protein changes areexpressed on a dry weight basis. The moisture content of each sample wasmeasured in the 2004 experiment. For the 2003 data, a moisture contentof 13% was assumed, to calculate the dry weight values. For the datashown in Table 14, a range of 1.0% to 3.5% was observed for the percentincrease in oil and protein. TABLE 14 Seed Composition of Field GrownHomozygous pPGM-Silenced (PGM-KO) and PGM-Wild-Type (PGM-WT) Seeds.Elite % % % Oil & Back- Pheno- Pro- % Oil Protein Protein ground Yeartype % Oil tein Increase Increase Increase 92B63 2003 PGM-KO 22.7 40.61.3 −0.3   1.0 92B63 2003 PGM-WT 21.4 40.9 — — — 92B63 2004 PGM-KO 19.142.2 1.1 0.5 1.6 92B63 2004 PGM-WT 18.0 41.7 — — — 92B91 2003 PGM-KO25.7 39.4 2.5 1.0 3.5 92B91 2003 PGM-WT 23.2 38.4 — — — 92B91 2004PGM-KO 21.4 40.2 1.7 0.3 2.0 92B91 2004 PGM-WT 19.7 39.9 — — — 93B872003 PGM-KO 23.1 40.2 0.7 1.2 1.9 93B87 2003 PGM-WT 22.4 39.0 — — —93B87 2004 PGM-KO 21.5 42.4 1.4 0.8 2.2 93B87 2004 PGM-WT 20.1 41.6 — ——

Example 14 Characterization of Defatted Meal from Transgenic SoybeanSeeds with Silenced Plastidic Phosphoglucomutase (pPGM).

T2 soybean seeds were ground to a fine powder and oil was extractedusing heptane. Approximately 200 mg of soybean seed were weighed andtransferred into pre-weighed 10 ml glass screw cap tubes. Two ml ofheptane were added and the mixture was vortexed for 15 min at roomtemperature. The glass tubes were centrifuged at 3500 rpm for 20 minutesand the heptane was carefully decanted into a new, pre-weighed glasstube. The pellet was re-extracted another three times as described aboveand all supernatants were pooled. The hexane was removed by evaporationusing a speedvac. Total oil content was determined gravimetrically.

An aliquot of the defatted meal was used for protein determination.About 60 mg of meal was transferred to a 15 ml polypropylene tube and 10ml 0.1 N NaOH were added and the mixture was incubated at 60° C. for 1hr. One ml of the suspension was transferred to a 2 ml eppendorf tubeand centrifuged at 14,000 rpm for 3 minutes. The supernatant was dilutedseveral fold and the protein content was determined using a microplateassay based on Sigma Total Protein Protocol (Procedure 541-2, Sigma).

The soluble carbohydrate profile of defatted soybean meal from T2 seedsis shown in FIG. 5. Sucrose to RFO ratios of 0.82 and 0.87 were observedfor the pPGM-suppressed event, 108-3-1-1.

The percent oil and percent protein content of defatted meal from T2Seeds of event 108-3-1-1 was determined on a wet-weight basis and ispresented in Table 15. A percent increase in combined oil and protein of3.02% and 4.82% was observed for defatted meal from a pPGM-suppressedline grown in the growth chamber and in the field, respectively.

The percent oil and percent protein content of defatted meal from T2Seeds of event 108-3-1-1 was determined on a dry-weight basis and ispresented in Table 16. A percent increase in combined oil and protein of3.20% and 5.17% was observed for defatted meal from a pPGM-suppressedline grown in the growth chamber and in the field, respectively. TABLE15 Characterization of Defatted Meal (wet-weight basis) from T2 Seeds ofEvent 108-3-1-1 from a pPGM Co-suppressed Events (PGM-KO) and a NullSegregant (PGM-WT) % Growth % % Oil & Con- Pheno- Pro- % Oil ProteinProtein ID dition type % Oil tein Increase Increase Increase 2097-7Growth PGM-KO 18.82 37.54 3.40 −0.38   3.02 Cham- ber 2097-7 FieldPGM-KO 17.65 40.51 2.23 2.59 4.82 2097-1 Field PGM-WT 15.42 37.92 — — —92B91 Field wild-type 16.92 36.80 — — —

TABLE 16 Characterization of Defatted Meal (dry-weight basis) from T2seeds of Event 108-1-1 from a pPGM Co-suppressed Event (PGM-KO) and aNull Segregant (PGM-WT) % Growth % % Oil & Con- Pheno- Pro- % OilProtein Protein ID dition type % Oil tein Increase Increase Increase2097-7 Growth PGM-KO 18.82 40.31 3.40 −0.20   3.20 Cham- ber 2097-7Field PGM-KO 17.65 43.45 2.23 2.94 5.17 2097-1 Field PGM-WT 15.42 40.51— — — 92B91 Field wild-type 16.92 39.35 — — —

Example 15 Characterization of cDNA Clones Encoding the Large Subunitand the Small Subunit Polypeptides of Soybean ADP-GlucosePyrophosphorylase

A BLAST analysis of soybean sequences identified cDNA clones thatencoded proteins with high sequence similarity to the large subunit ofADP-glucose pyrophosphorylase from chickpea, Cicer arietinum (NCBIGeneral Identifier No. 13487785), and to the small subunit, PvAGPS1, ofADP-glucose pyrophosphorylase from Phaseolus vulgaris (NCBI GeneralIdentifier No. 29421116). SEQ ID NO:24, encoded by SEQ ID NO:23,corresponds to the amino acid sequence of a large subunit polypeptide ofsoybean ADP-glucose pyrophosphorylase and has a pLog score of greaterthan 254 when compared to the large subunit of ADP-glucosepyrophosphorylase from chickpea (SEQ ID NO:25; GI No. 13487785). SEQ IDNO:28, encoded by SEQ ID NO:27, corresponds to the amino acid sequenceof a first small subunit polypeptide (SS1) of soybean ADP-glucosepyrophosphorylase and has a pLog score of greater than 254 when comparedto the small subunit polypeptide, PvAGPS1, of ADP-glucosepyrophosphorylase from Phaseolus vulgaris (SEQ ID NO:31; GI No.29421116). SEQ ID NO:30, encoded by SEQ ID NO:29, corresponds to theamino acid sequence of a second small subunit polypeptide (SS2) ofsoybean ADP-glucose pyrophosphorylase and has a pLog score of greaterthan 254 when compared to the small subunit polypeptide, PvAGPS1, ofADP-glucose pyrophosphorylase from Phaseolus vulgaris (SEQ ID NO:31; GINo. 29421116).

The large subunit amino acid sequences of SEQ ID NOs:24, 25 and 26 werealigned and the percent sequence identities were calculated for eachpair of sequences. The soybean large subunit amino acid sequence of SEQID NO:24 is 79.1% identical to the large subunit of ADP-glucosepyrophosphorylase from chickpea (SEQ ID NO:25; GI No.13487785), and is99.6% identical to SEQ ID NO:26 (SEQ ID NO:248406 from U.S. patentapplication US2004031072).

The small subunit amino acid sequences of SEQ ID NOs:28, 30, 31 and 32were aligned and the percent sequence identities were calculated foreach pair of sequences. The soybean small subunit SS1 amino acidsequence of SEQ ID NO:28 is 94.6% identical to the small subunitpolypeptide, PvAGPS1, of ADP-glucose pyrophosphorylase from Phaseolusvulgaris (SEQ ID NO:31; GI No. 29421116), and is 98.3% identical to SEQID NO:32 (SEQ ID NO:251944 from U.S. patent application US2004031072).The soybean small subunit SS2 amino acid sequence of SEQ ID NO:30 is94.0% identical to the small subunit polypeptide, PvAGPS1, ofADP-glucose pyrophosphorylase from Phaseolus vulgaris (SEQ ID NO:31; GINo. 29421116), and is 100% identical to SEQ ID NO:32 (SEQ ID NO:251944from U.S. patent application US2004031072). The soybean small subunitSS1 polypeptide (SEQ ID NO:28) and the SS2 polypeptide (SEQ ID NO:30)have 98.3% sequence identity with each other.

Sequence alignments and percent identity calculations were performedusing the Megalign program of the LASERGENE bioinformatics computingsuite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequenceswas performed using the Clustal V method of alignment (Higgins and Sharp(1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10,GAP LENGTH PENALTY=10). Default parameters for pairwise alignments usingthe Clustal method were KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALSSAVED=5.

Sequence alignments and BLAST scores and probabilities indicate that thenucleic acid fragments comprising the instant cDNA clones encodefull-length polypeptides for the large and small subunits of ADP-glucosepyrophosphorylase from soybean.

1. An isolated polynucleotide comprising: (a) a first nucleotidesequence encoding a first polypeptide having phosphoglucomutaseactivity, wherein the amino acid sequence of the first polypeptide andthe amino acid sequence of SEQ ID NO:8 have at least 95% identity basedon the Clustal alignment method, (b) a second nucleotide sequenceencoding a second polypeptide having phosphoglucomutase activity,wherein the amino acid sequence of the second polypeptide and the aminoacid sequence of SEQ ID NO:2 or SEQ ID NO:4 have at least 85% identitybased on the Clustal alignment method, or (c) the complement of thefirst or second nucleotide sequence.
 2. The isolated polynucleotide ofclaim 1 wherein the amino acid sequence of the second polypeptide andthe amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4 have at least 90%identity based on the Clustal alignment method.
 3. The isolatedpolynucleotide of claim 1, wherein the amino acid sequence of the secondpolypeptide and the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4have at least 95% identity based on the Clustal alignment method.
 4. Theisolated polynucleotide of claim 1, wherein the first polypeptidecomprises the amino acid sequence of SEQ ID NO:8, wherein the secondpolypeptide comprises the amino acid sequence of SEQ ID NO:2 or SEQ IDNO:4.
 5. The isolated polynucleotide of claim 1, wherein the firstnucleotide sequence comprises the nucleotide sequence of SEQ ID NO:7,wherein the second nucleotide sequence comprises the nucleotide sequenceof SEQ ID NO:1 or SEQ ID NO:3.
 6. A recombinant DNA construct comprisingthe polynucleotide of claim 1 operably linked to a regulatory sequence.7. A method for transforming a cell comprising transforming a cell withthe polynucleotide of claim
 1. 8. A cell comprising the recombinant DNAconstruct of claim
 6. 9. A method for producing a transgenic plantcomprising transforming a plant cell with the polynucleotide of claim 1and regenerating a plant from the transformed plant cell.
 10. A plantcomprising the recombinant DNA construct of claim
 6. 11. A seedcomprising the recombinant DNA construct of claim
 6. 12. An isolatedpolypeptide having phosphoglucomutase activity, wherein the polypeptidecomprises: (a) a first amino acid sequence, wherein the first amino acidsequence and the amino acid sequence of SEQ ID NO:8 have at least 95%identity based on the Clustal alignment method, or (b) a second aminoacid sequence, wherein the second amino acid sequence and the amino acidsequence of SEQ ID NO:2 or SEQ ID NO:4 have at least 85% identity basedon the Clustal alignment method.
 13. The polypeptide of claim 12,wherein the second amino acid sequence and the amino acid sequence ofSEQ ID NO:2 or SEQ ID NO:4 have at least 90% identity based on theClustal alignment method.
 14. The polypeptide of claim 12, wherein thesecond amino acid sequence and the amino acid sequence of SEQ ID NO:2 orSEQ ID NO:4 have at least 95% identity based on the Clustal alignmentmethod.
 15. The polypeptide of claim 12, wherein the first amino acidsequence comprises the amino acid sequence of SEQ ID NO:8, and whereinthe second amino acid sequence comprises the amino acid sequence of SEQID NO:2 or SEQ ID NO:4.
 16. A method of selecting an isolatedpolynucleotide that decreases the level of expression of a plastidicpolypeptide having phosphoglucomutase activity in a plant cell, themethod comprising the steps of: (a) constructing the isolatedpolynucleotide comprising a nucleotide sequence of at least 30contiguous nucleotides derived from the isolated polynucleotide of claim1; (b) introducing the isolated polynucleotide into the plant cell; (c)measuring the level of the polypeptide in the plant cell containing thepolynucleotide; and (d) comparing the level of the polypeptide in theplant cell containing the isolated polynucleotide with the level of thepolypeptide in a plant cell that does not contain the isolatedpolynucleotide; and selecting the isolated polynucleotide that decreasesthe level of expression of the plastidic polypeptide havingphosphoglucomutase activity in the plant cell.
 17. The method of claim16 wherein the isolated polynucleotide comprises a nucleotide sequenceselected from the group consisting of SEQ ID NOs:1, 3 and
 7. 18. Themethod of claim 16 wherein the isolated polynucleotide comprising anucleotide sequence of at least 30 contiguous nucleotides contains atleast 541 nucleotides.
 19. The method of claim 16 wherein the isolatedpolynucleotide comprises the nucleotide sequence of SEQ ID NO:15.
 20. Amethod of selecting an isolated polynucleotide that increases the levelof expression of a plastidic polypeptide having phosphoglucomutaseactivity in a plant cell, the method comprising the steps of: (a)constructing the isolated polynucleotide of claim 1; (b) introducing theisolated polynucleotide into the plant cell; (c) measuring the level ofthe polypeptide in the plant cell containing the polynucleotide; (d)comparing the level of the polypeptide in the plant cell containing theisolated polynucleotide with the level of the polypeptide in a plantcell that does not contain the polynucleotide; and selecting theisolated polynucleotide that increases the level of expression of theplastidic polypeptide having phosphoglucomutase activity in the plantcell.
 21. A method for positive selection of a transformed cellcomprising: (a) transforming a host cell with the recombinant DNAconstruct of claim 6; and (b) growing the transformed host cell underconditions which allow expression of a polynucleotide in an amountsufficient to complement a null mutant to provide a positive selectionmeans.
 22. The method of claim 21 wherein the host cell is a plant. 23.The method of claim 21 wherein the plant cell is a monocot.
 24. Themethod of claim 21 wherein the plant cell is a dicot.
 25. A method ofincreasing the level of expression of a plastidic polypeptide havingphosphoglucomutase activity in a host cell comprising: (a) transforminga host cell with the recombinant DNA construct of claim 6; and (b)growing the transformed host cell from step (a) under conditions thatare suitable for expression of the recombinant DNA construct; and (c)selecting a transformed cell wherein expression of the recombinant DNAconstruct results in production of higher levels of a plastidicpolypeptide having phosphoglucomutase activity in the transformed hostcell.
 26. A method for suppressing the level of expression of a geneencoding a plastidic polypeptide having phosphoglucomutase activity in atransgenic plant, wherein the method comprises: (a) transforming a plantcell with a fragment of the isolated polynucleotide of claim 1; (b)regenerating a transgenic plant from the transformed plant cell of (a);and (c) selecting a transgenic plant wherein the level of expression ofa gene encoding a plastidic polypeptide having phosphoglucomutaseactivity has been suppressed.
 27. A recombinant DNA constructcomprising: (a) all or part of the nucleotide sequence set forth in SEQID NO:7 or SEQ ID NO:15; (b) the complement of (a); wherein (a) or (b)is useful in co-suppression or antisense suppression of endogenousphosphoglucomutase activity in a transgenic plant.
 28. A method forproducing transgenic seed, the method comprising: (a) transforming aplant cell with the recombinant DNA construct of claim 27; (b)regenerating a transgenic plant from the transformed plant cell of (a);and (c) selecting a transgenic plant that produces a transgenic seedhaving an increase in the combined oil and protein content of at least1.6% and a decrease in the sucrose content of at least 25% as comparedto seed obtained from a non-transgenic plant.
 29. The method of claim 28wherein the increase in the combined oil and protein content is at least1.8%.
 30. The method of claim 28 wherein the increase in the combinedoil and protein content is at least 2.0%.
 31. A method for producingtransgenic seed, the method comprising: (a) transforming a plant cellwith the recombinant DNA construct of claim 27; (b) regenerating atransgenic plant from the transformed plant cell of (a); and (c)selecting a transgenic plant that produces a transgenic seed having asucrose to raffinose family oligosaccharide ratio of 1.0 or less ascompared to seed obtained from a non-transgenic plant.
 32. The method ofclaim 31 wherein the transgenic seed differs from a non-transgenic seedby having an increase in the combined oil and protein content of atleast 1.6%.
 33. The method of claim 31wherein the transgenic seeddiffers from a non-transgenic seed by having an increase in the combinedoil and protein content of at least 1.8%.
 34. The method of claim 31wherein the transgenic seed differs from a non-transgenic seed by havingan increase in the combined oil and protein content of at least 2.0%.35. A method for producing defatted meal from transgenic seed, themethod comprising: (a) transforming a plant cell with the recombinantDNA construct of claim 27; (b) regenerating a transgenic plant from thetransformed plant cell of (a); and (c) selecting a transgenic plant thatproduces a transgenic seed wherein said seed is processed into defattedmeal having an increase in the combined oil and protein content of atleast 5% and a decrease in the sucrose content of at least 25% ascompared to defatted meal obtained from seed of a non-transgenic plant.36. The method of claim 35 wherein the defatted meal of the transgenicseed has a sucrose to raffinose family oligosaccharide ratio of 1.0 orless as compared to the sucrose to raffinose family oligosaccharideratio of defatted meal obtained from a non-transgenic seed.
 37. Themethod of any one of claims 28-36 wherein the transgenic seed isobtained from a transgenic dicot plant comprising in its genome therecombinant construct.
 38. The method of claim 37 wherein the dicotplant is selected from the group consisting of Arabidopsis, soybean,oilseed Brassica, peanut, sunflower, safflower, cotton, tobacco, tomato,potato, and cocoa.
 39. The method of claim 37 wherein the dicot plant issoybean.
 40. A transgenic seed comprising the recombinant DNA constructof claim 27 in its genome wherein said transgenic seed has an increasein the combined oil and protein content of at least 1.6% and a decreasein the sucrose content of at least 25% when compared to a non-transgenicseed.
 41. The transgenic seed of claim 40 wherein the increase in thecombined oil and protein content is at least 1.8%.
 42. The transgenicseed of claim 40 wherein the increase in the combined oil and proteincontent is at least 2.0%.
 43. A transgenic seed comprising therecombinant DNA construct of claim 27 in its genome wherein saidtransgenic seed has a sucrose to raffinose family oligosaccharide ratioof 1.0 or less when compared to a non-transgenic seed.
 44. Thetransgenic seed of claim 43 wherein the transgenic seed has an increasein the combined oil and protein content of at least 1.6% when comparedto a non-transgenic seed.
 45. The transgenic seed of claim 43 whereinthe transgenic seed has an increase in the combined oil and proteincontent of at least 1.8% when compared to a non-transgenic seed.
 46. Thetransgenic seed of claim 43 wherein the transgenic seed has an increasein the combined oil and protein content of at least 2.0% when comparedto a non-transgenic seed.
 47. Transgenic seed comprising the recombinantconstruct of claim 27 in its genome wherein said transgenic seed isprocessed to make defatted meal having an increase in the combined oiland protein content of at least 5% and a decrease in the sucrose contentof at least 25% when compared to defatted meal obtained from anon-transgenic seed.
 48. The transgenic seed of claim 47 wherein thedefatted meal of the transgenic seed differs from the defatted meal of anon-transgenic seed by having a sucrose to raffinose familyoligosaccharide ratio of 1.0 or less.
 49. The transgenic seed of any oneof claims 40-48 wherein the seed is a soybean seed.